6O9L: Human holo-PIC in the closed state

Human holo-PIC in the closed state. Determined by electron microscopy at 7.2 Å resolution. Released 29 May 2019.

Method: Electron microscopy
Resolution: 7.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 33
Atoms: 81,800
Mol. weight: 1379.42 kDa
Ligands: SF4, ZN, MG
Released: 29 May 2019

Explore 6O9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O9L contains 402 α-helices and 373 β-strands across 31 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 36 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	16-17	2
α-helix	21-34	14
β-strand	38-41	4	109
α-helix	50-60	11
β-strand	71-74	4	109
α-helix	77-97	21
α-helix	101-103	3
β-strand	106-108	3	109
α-helix	112-114	3
α-helix	128-136	9
α-helix	137-141	5
α-helix	156-166	11
β-strand	175	1	109
α-helix	177-185	9
α-helix	191-199	9
β-strand	204-208	5	109
β-strand	230-232	3	109
α-helix	242-245	4
β-strand	249-252	4	110
α-helix	253-271	19
α-helix	276-290	15
α-helix	295-297	3
α-helix	300-303	4
α-helix	325-337	13
α-helix	339-346	8
α-helix	354-364	11
α-helix	371-386	16
α-helix	391-408	18
β-strand	417-418	2	110
β-strand	432-435	4	110
α-helix	445-450	6
β-strand	453-458	6	109
α-helix	467-469	3
β-strand	476-478	3	109
β-strand	492-495	4	111
α-helix	515-527	13
β-strand	535-539	5	111
α-helix	542-555	14
α-helix	558-564	7
α-helix	566	1
β-strand	567-569	3	111
α-helix	575-590	16
β-strand	595-599	5	111
β-strand	617-621	5	111
α-helix	631-638	8
α-helix	640-643	4
α-helix	646-648	3
α-helix	650-664	15
β-strand	676-680	5	111
α-helix	687-689	3
α-helix	694-697	4
β-strand	708	1	111
α-helix	710-723	14
α-helix	739-741	3

Chain 1: 30 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	12	1	112
β-strand	15-16	2	102
β-strand	24	1	112
β-strand	25-26	2	113
β-strand	31-33	3	113
β-strand	43-44	2	113
β-strand	53-54	2	102
β-strand	64-68	5	102
β-strand	74-79	6	102
α-helix	89-95	7
α-helix	116-119	4
α-helix	122-131	10
α-helix	139-141	3
α-helix	142-146	5
α-helix	151-154	4
α-helix	156-158	3
α-helix	194-199	6
α-helix	201-208	8
α-helix	217-219	3
α-helix	221-224	4
α-helix	239-260	22
α-helix	266-274	9
α-helix	296-299	4
α-helix	301-319	19
α-helix	332-334	3
α-helix	351-362	12
α-helix	364-366	3
α-helix	375-384	10
α-helix	391-408	18
α-helix	410-413	4
α-helix	418-434	17
α-helix	449-451	3
α-helix	457-476	20
α-helix	489-503	15
α-helix	505-508	4
α-helix	515-518	4
α-helix	519-521	3
α-helix	526-538	13

Chain 2: 30 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-23	9
α-helix	28-34	7
α-helix	37-40	4
α-helix	50-61	12
β-strand	66-67	2	114
α-helix	69-74	6
α-helix	80-83	4
α-helix	87-93	7
β-strand	96-98	3	114
β-strand	107-110	4	114
α-helix	112-120	9
α-helix	128-130	3
α-helix	145-164	20
α-helix	176-180	5
α-helix	200-206	7
α-helix	210-216	7
α-helix	219-222	4
α-helix	228-235	8
α-helix	238-240	3
α-helix	249-252	4
α-helix	256-266	11
β-strand	271-273	3	115
α-helix	275-277	3
β-strand	281-283	3	115
α-helix	288-292	5
α-helix	325-331	7
α-helix	350-355	6
α-helix	362-369	8
α-helix	375-378	4
α-helix	387-396	10
α-helix	397-399	3
β-strand	404-409	6	116
α-helix	416-428	13
β-strand	431-435	5	116
β-strand	440-443	4	116
α-helix	445-447	3
α-helix	448-457	10

Chain 3: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	117
β-strand	29-31	3	117
α-helix	32-39	8
β-strand	61	1	117
α-helix	69-77	9
α-helix	78-82	5
α-helix	85-88	4
α-helix	99-108	10
α-helix	116-123	8
α-helix	133-184	52
α-helix	196-213	18
α-helix	254-256	3
α-helix	269-274	6
α-helix	291-301	11

Chain 4: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	118
α-helix	19-25	7
α-helix	26-28	3
α-helix	34-51	18
β-strand	56-61	6	118
β-strand	69-71	3	118
α-helix	103-120	18
α-helix	134-151	18
β-strand	158-163	6	118
β-strand	164	1	119
α-helix	175-185	11
β-strand	191	1	118
β-strand	193-195	3	119
α-helix	205-209	5
β-strand	214-216	3	119
α-helix	245-247	3
β-strand	267	1	120
β-strand	274	1	120
α-helix	294-297	4

Chain 5: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	116
β-strand	10-11	2	29
α-helix	14-16	3
α-helix	17-24	8
β-strand	37-39	3	29
β-strand	42-43	2	29
α-helix	47-49	3
α-helix	50-53	4
α-helix	54-56	3
α-helix	57-64	8

Chain 6: 15 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	25-27	3
α-helix	33-42	10
β-strand	60	1	54
β-strand	63-66	4	55
α-helix	81-98	18
β-strand	103	1	54
β-strand	104	1	56
β-strand	106-109	4	55
β-strand	110	1	57
β-strand	113	1	57
β-strand	116	1	55
β-strand	121	1	56
α-helix	124-132	9
α-helix	133-135	3
α-helix	145-156	12
β-strand	166-170	5	55
α-helix	183-189	7
β-strand	195-200	6	55
α-helix	209-214	6
β-strand	219-221	3	55
α-helix	225-234	10
α-helix	238-239	2
β-strand	253	1	58
β-strand	258	1	59
β-strand	271	1	60
β-strand	285	1	60
β-strand	288	1	59
β-strand	289-290	2	61
β-strand	297-298	2	61
β-strand	312	1	58
α-helix	319-324	6
β-strand	332-333	2	62
β-strand	345	1	63
β-strand	349	1	63
β-strand	358-359	2	62
β-strand	367	1	62
α-helix	369-374	6
α-helix	375-379	5
α-helix	383-385	3

Chain 7: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	61-64	4
β-strand	84-85	2	67
α-helix	95-102	8
β-strand	118-119	2	67
α-helix	133-143	11
β-strand	166	1	68
β-strand	174	1	68
α-helix	182-185	4
α-helix	279-288	10
α-helix	318-327	10
β-strand	337-338	2	69
α-helix	346-357	12
β-strand	362-364	3	69
α-helix	369-377	9
α-helix	384-386	3
β-strand	407-408	2	69
α-helix	421-428	8
α-helix	430-433	4
β-strand	437-441	5	69
α-helix	448-457	10
β-strand	462-466	5	69
β-strand	487-489	3	69
α-helix	493-497	5
β-strand	506	1	70
β-strand	507-512	6	71
α-helix	513-515	3
α-helix	516-519	4
α-helix	528-530	3
α-helix	531-535	5
α-helix	538-552	15
β-strand	558-561	4	71
α-helix	570-573	4
α-helix	586-594	9
β-strand	605-607	3	71
β-strand	620	1	72
β-strand	622-625	4	71
α-helix	635-643	9
β-strand	644	1	72
β-strand	659-664	6	71
α-helix	670-673	4
α-helix	675-680	6
β-strand	686	1	70
β-strand	689-690	2	71
α-helix	706-711	6
α-helix	713-716	4

23 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA-directed RNA polymerase II subunit RPB1	A	protein	1970	Homo sapiens	P24928 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2	B	protein	1174	Homo sapiens	P30876 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3	C	protein	275	Homo sapiens	P19387 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4	D	protein	142	Homo sapiens	O15514 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB5	E	protein	210	Homo sapiens	P19388
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	protein	127	Homo sapiens	P61218
DNA-directed RNA polymerase II subunit RPB7	G	protein	172	Homo sapiens	P62487
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	protein	150	Homo sapiens	P52434
DNA-directed RNA polymerase II subunit RPB9	I	protein	125	Homo sapiens	P36954
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	protein	67	Homo sapiens	P62875
DNA-directed RNA polymerase II subunit RPB11-a	K	protein	117	Homo sapiens	P52435
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	protein	58	Homo sapiens	P53803

21 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6O9L_1 DNA-directed RNA polymerase II subunit RPB1 (chains A)
MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVD
SNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKG
HGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP
RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAA
HVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVD
FSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYII
RDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS
TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD
TLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHI
NCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEM
GHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA
HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKIN
ISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHA
MGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGES
VEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR
EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKL
VIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAI
AHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLT
VFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP
DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIR
IMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKI
IITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALER
ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM
EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTG
MFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPG
YSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP
TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS
YSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPT
SPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPASPKYTPTSPSYSPSSPEYTPTSPKY
SPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS
PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN

Sequence of entity 2 (B), FASTA

>6O9L_2 DNA-directed RNA polymerase II subunit RPB2 (chains B)
MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVE
DAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTY
SAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLD
PGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML
ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEM
VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETK
KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQ
KFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS
HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSP
ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE
VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASG
VVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP
RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIV
AIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGM
RHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSE
TGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGY
HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGC
RNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV

Sequence of entity 3 (C), FASTA

>6O9L_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN

Sequence of entity 4 (D), FASTA

>6O9L_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY

Sequence of entity 5 (E), FASTA

>6O9L_5 DNA-directed RNA polymerase II subunit RPB5 (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Sequence of entity 6 (F), FASTA

>6O9L_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIITD

Sequence of entity 7 (G), FASTA

>6O9L_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Sequence of entity 8 (H), FASTA

>6O9L_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Sequence of entity 9 (I), FASTA

>6O9L_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE

Sequence of entity 10 (J), FASTA

>6O9L_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK

Sequence of entity 11 (K), FASTA

>6O9L_11 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Sequence of entity 12 (L), FASTA

>6O9L_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
ZN	Zinc ion	Zn	17
MG	Magnesium ion	Mg	2

Primary citation

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Yan, C., Dodd, T., He, Y. et al. Nat Struct Mol Biol (2019) 26:397-406. DOI 10.1038/s41594-019-0220-3 · PubMed

Other PDB entries of the same protein (UniProt P24928 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6G0R 1.25 Å, Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated…
7Z1K 1.55 Å, Crystal structure of the SPOC domain of human SHARP (SPEN) in complex with RNA…
3D9N 1.6 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
6XKB 1.6 Å, Crystal structure of SR-related and CTD-associated factor 4(SCAF4-CID)with peptide…
6IC9 1.75 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
3D9M 1.75 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
2GHT 1.8 Å, CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA…
4JXT 1.9 Å, CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD
6IC8 1.93 Å, Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD…
3D9O 2.0 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…
2GHQ 2.05 Å, CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA…
3D9P 2.1 Å, Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of…

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