6YBT: PDB entry 6YBT

Name: PDB 6YBT: Structure of a human 48S translational initiation complex - eIF3bgi
Published: 2020-09-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of a human 48S translational initiation complex - eIF3bgi. Determined by electron microscopy at 6.0 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 6.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,426
Mol. weight: 292.32 kDa
Released: 16 Sept 2020

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

Secondary structure: helices and β-sheets

6YBT contains 23 α-helices and 73 β-strands across 3 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 1: 17 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	180	1	9
β-strand	187-190	4	10
α-helix	199-202	4
α-helix	207-210	4
α-helix	212-214	3
β-strand	217-219	3	11
β-strand	225	1	12
β-strand	228	1	12
α-helix	229-230	2
β-strand	232-235	4	10
β-strand	236-237	2	11
α-helix	240-242	3
α-helix	243-249	7
β-strand	264	1	10
β-strand	268	1	9
α-helix	287-291	5
α-helix	295-298	4
β-strand	308-310	3	13
α-helix	311-313	3
β-strand	315-319	5	13
β-strand	328-332	5	13
β-strand	338-342	5	14
β-strand	349-353	5	14
β-strand	356-361	6	14
β-strand	366-372	7	14
β-strand	378-381	4	15
β-strand	388-396	9	15
β-strand	402-407	6	15
β-strand	414-417	4	15
β-strand	429-431	3	16
β-strand	438-442	5	16
β-strand	445-447	3	16
β-strand	450	1	17
β-strand	455	1	17
α-helix	460-463	4
β-strand	465	1	16
β-strand	469-472	4	18
β-strand	479-483	5	18
α-helix	484-486	3
β-strand	491-496	6	18
β-strand	503-509	7	18
β-strand	515-519	5	19
β-strand	525-531	7	19
β-strand	542-548	7	19
β-strand	556-560	5	19
β-strand	565-570	6	20
α-helix	571	1
β-strand	576-581	6	20
α-helix	584-586	3
β-strand	587-594	8	20
β-strand	600-609	10	20
β-strand	613-616	4	21
β-strand	623-626	4	21
β-strand	638	1	21
β-strand	656-659	4	22
β-strand	666-669	4	22
β-strand	680-683	4	22
β-strand	692-695	4	22
α-helix	704-706	3
α-helix	714-717	4
α-helix	738-744	7
α-helix	749-763	15

Chain 2: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	1
β-strand	13-18	6	2
β-strand	24-29	6	2
β-strand	34-38	5	2
β-strand	46-48	3	2
β-strand	55-57	3	3
β-strand	60	1	3
β-strand	67-71	5	3
β-strand	75-79	5	3
β-strand	90-91	2	3
β-strand	101	1	4
β-strand	107-111	5	4
β-strand	122-126	5	4
β-strand	128	1	5
α-helix	129-131	3
β-strand	133	1	5
β-strand	140-142	3	4
β-strand	153-154	2	6
α-helix	156-158	3
β-strand	160-164	5	6
β-strand	170-174	5	6
β-strand	179-180	2	6
β-strand	206	1	7
β-strand	212-214	3	7
β-strand	224-226	3	7
α-helix	237-238	2
β-strand	243-244	2	8
β-strand	265-271	7	8
β-strand	277-284	8	8
β-strand	301-303	3	1
β-strand	309-311	3	1

Chain u: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	574-637	64
α-helix	655-705	51

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 3 subunit A	u	protein	1350	Homo sapiens	Q14152 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit I	2	protein	325	Homo sapiens	Q13347 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit B	1	protein	814	Homo sapiens	P55884 (AlphaFold model)

Sequence of entity 1 (u), FASTA

>6YBT_1 Eukaryotic translation initiation factor 3 subunit A (chains u)
DVMKSKKHRTWQKIHEPIMLKYLELCVDLRKSHLAKEGLYQYKNICQQVNIKSLEDVVRA
YLKMAEEKTEAAKEESQQMVLDIEDLDNIQTPESVLLSAVSGEDTQDRTDRLLLTPWVKF
LWESYRQCLDLLRNNSRVERLYHDIAQQAFKFCLQYTRKAEFRKLCDNLRMHLSQIQRHH
NQSTAINLNNPESQSMHLETRLVQLDSAISMELWQEAFKAVEDIHGLFSLSKKPPKPQLM
ANYYNKVSTVFWKSGNALFHASTLHRLYHLSREMRKNLTQDEMQRMSTRVLLATLSIPIT
PERTDIARLLDMDGIIVEKQRRLATLLGLQAPPTRIGLINDMVRFNVLQYVVPEVKDLYN
WLEVEFNPLKLCERVTKVLNWVREQPEKEPELQQYVPQLQNNTILRLLQQVSQIYQSIEF
SRLTSLVPFVDAFQLERAIVDAARHCDLQVRIDHTSRTLSFGSDLNYATREDAPIGPHLQ
SMPSEQIRNQLTAMSSVLAKALEVIKPAHILQEKEEQHQLAVTAYLKNSRKEHQRILARR
QTIEERKERLESLNIQREKEELEQREAELQKVRKAEEERLRQEAKEREKERILQEHEQIK
KKTVRERLEQIKKTELGAKAFKDIDIEDLEELDPDFIMAKQVEQLEKEKKELQERLKNQE
KKIDYFERAKRLEEIPLIKSAYEEQRIKDMDLWEQQEEERITTMQLEREKALEHKNRMSR
MLEDRDLFVMRLKAARQSVYEEKLKQFEERLAEERHNRLEERKRQRKEERRITYYREKEE
EEQRRAEEQMLKEREERERAERAKREEELREYQERVKKLEEVERKKRQRELEIEERERRR
EEERRLGDSSLSRKDSRWGDRDSEGTWRKGPEADSEWRRGPPEKEWRRGEGRDEDRSHRR
DEERPRRLGDDEDREPSLRPDDDRVPRRGMDDDRGPRRGPEEDRFSRRGADDDRPSWRNT
DDDRPPRRIADEDRGNWRHADDDRPPRRGLDEDRGSWRTADEDRGPRRGMDDDRGPRRGG
ADDERSSWRNADDDRGPRRGLDDDRGPRRGMDDDRGPRRGMDDDRGPRRGMDDDRGPRRG
LDDDRGPWRNADDDRIPRRGAEDDRGPWRNMDDDRLSRRADDDRFPRRGDDSRPGPWRPL
VKPGGWREKEKAREESWGPPRESRPSEEREWDREKERDRDNQDREENDKDPERERDRERD
VDREDRFRRPRDEGGWRRGPAEESSSWRDSSRRDDRDRDDRRRERDDRRDLRERRDLRDD
RDRRGPPLRSEREEVSSWRRADDRKDDRVEERDPPRRVPPPALSRDRERDRDREREGEKE
KASWRAEKDRESLRRTKNETDEDGWTTVRR

Sequence of entity 2 (2), FASTA

>6YBT_2 Eukaryotic translation initiation factor 3 subunit I (chains 2)
MKPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDA
DWDTKHVLTGSADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQC
FVSFFDLRDPSQIDNNEPYMKIPCNDSKITSAVWGPLGECIIAGHESGELNQYSAKSGEV
LVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTTLEHQKTFRTERPVNSAALSPN
YDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRVKGHFGPINSVAFHPDGKSY
SSGGEDGYVRIHYFDPQYFEFEFEA

Sequence of entity 3 (1), FASTA

>6YBT_3 Eukaryotic translation initiation factor 3 subunit B (chains 1)
MQDAENVAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAGTEASSEEVGIAEA
GPESEVRTEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQARDERSDSR
AQAVSEDAGGNEGRAAEAEPRALENGDADEPSFSDPEDFVDDVSEEELLGDVLKDRPQEA
DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASP
AHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMTISDEWDIPEKQPFKDLGNLRYWLEEA
ECRDQYSVIFESGDRTSIFWNDVKDPVSIEERARWTETYVRWSPKGTYLATFHQRGIALW
GGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQAIIIWDILTGHKKRGFHC
ESSAHWPIFKWSHDGKFFARMTLDTLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA
FWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDRTPKGTQGV
VTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKNNGKI
ELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWD
PTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQI
KKDLKKYSKIFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMEQKNERLELRG
GVDTDELDSNVDDWEEETIEFFVTEEIIPLGNQE

Primary citation

Structure of a human 48Stranslational initiation complex. Brito Querido, J., Sokabe, M., Kraatz, S. et al. Science (2020) 369:1220-1227. DOI 10.1126/science.aba4904 · PubMed

Other PDB entries of the same protein (UniProt Q14152 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
9KZU 3.0 Å, Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome…
8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
9KN5 3.2 Å, Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
9KRP 3.2 Å, Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3
6YBD 3.3 Å, Structure of a human 48S translational initiation complex - eIF3

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