8B3I: CRL4CSA-E2-Ub

CRL4CSA-E2-Ub (state 2). Determined by electron microscopy at 3.5 Å resolution. Released 27 Sept 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 7
Atoms: 20,197
Mol. weight: 305.41 kDa
Ligands: ZN
Released: 27 Sept 2023

Explore 8B3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B3I contains 71 α-helices and 183 β-strands across 7 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 a: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
α-helix	15-28	14
β-strand	30-32	3	11
β-strand	37-38	2	12
β-strand	46-51	6	13
β-strand	58-63	6	13
β-strand	68-72	5	13
β-strand	83-84	2	12
β-strand	88-90	3	13
β-strand	102-107	6	14
α-helix	108	1
β-strand	114-119	6	14
β-strand	123-128	6	14
β-strand	134-139	6	14
β-strand	144-149	6	15
β-strand	158-163	6	15
β-strand	168-172	5	15
β-strand	181-182	2	15
β-strand	191-194	4	16
β-strand	201-205	5	16
β-strand	211-215	5	16
β-strand	224-225	2	16
β-strand	227	1	17
β-strand	248-253	6	18
β-strand	259-264	6	18
β-strand	268-273	6	18
β-strand	278	1	17
β-strand	279	1	18
β-strand	298-299	2	19
β-strand	307-312	6	19
β-strand	315-320	6	19
β-strand	326-330	5	19
β-strand	337-343	7	11
β-strand	348-353	6	11
β-strand	358-363	6	11

Chain d: 12 helices, 110 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	20
β-strand	15-21	7	21
β-strand	30-35	6	21
β-strand	38-41	4	21
β-strand	43	1	21
β-strand	53-56	4	21
β-strand	61-67	7	22
β-strand	76-81	6	22
β-strand	85-94	10	22
β-strand	97-107	11	22
α-helix	114	1
β-strand	115	1	23
α-helix	116	1
β-strand	121-124	4	24
β-strand	130-134	5	24
β-strand	136	1	23
β-strand	139-144	6	24
β-strand	155-158	4	24
β-strand	164-169	6	25
β-strand	177-184	8	25
β-strand	187-194	8	25
β-strand	204	1	25
β-strand	210-211	2	25
β-strand	220-221	2	26
β-strand	229-231	3	26
β-strand	237-240	4	26
β-strand	245-248	4	26
α-helix	252-254	3
β-strand	258-263	6	27
β-strand	270-275	6	27
β-strand	279-288	10	27
β-strand	296-307	12	27
β-strand	313-318	6	28
β-strand	321-325	5	28
β-strand	331-336	6	28
β-strand	347-353	7	28
β-strand	362-365	4	29
α-helix	367-369	3
β-strand	374-377	4	29
β-strand	386-387	2	30
β-strand	388	1	29
β-strand	390-391	2	31
β-strand	394	1	32
β-strand	396-403	8	33
β-strand	407-413	7	34
β-strand	424-429	6	34
β-strand	435-438	4	34
β-strand	443-446	4	34
β-strand	457	1	35
β-strand	463	1	36
β-strand	467	1	36
β-strand	470-471	2	36
β-strand	472	1	35
β-strand	475-480	6	36
β-strand	485-491	7	36
β-strand	500-503	4	37
β-strand	507-512	6	37
β-strand	515-522	8	37
β-strand	525-533	9	37
β-strand	538-542	5	38
β-strand	555-560	6	38
β-strand	565-570	6	38
β-strand	575-581	7	38
β-strand	588-596	9	39
β-strand	599-606	8	39
β-strand	610-615	6	39
β-strand	624-630	7	39
α-helix	635-636	2
β-strand	637-642	6	40
β-strand	647-652	6	40
β-strand	657-661	5	40
β-strand	666-670	5	40
β-strand	671	1	32
β-strand	678	1	33
β-strand	681-682	2	41
β-strand	690-691	2	41
β-strand	694	1	33
β-strand	698-704	7	33
β-strand	711-712	2	31
β-strand	715-716	2	30
β-strand	720-727	8	42
β-strand	732-741	10	42
β-strand	751	1	42
α-helix	756-758	3
β-strand	762-765	4	42
β-strand	786-795	10	42
β-strand	801-806	6	42
β-strand	811-819	9	43
β-strand	828-835	8	43
β-strand	846-847	2	44
β-strand	848-854	7	43
β-strand	857-862	6	43
β-strand	865-866	2	44
β-strand	874-876	3	45
β-strand	879-881	3	45
β-strand	884	1	46
β-strand	887	1	46
β-strand	890-893	4	45
β-strand	899-903	5	45
β-strand	911-917	7	47
β-strand	920-925	6	47
β-strand	932-936	5	47
β-strand	941-944	4	47
β-strand	947	1	48
β-strand	954-961	8	49
β-strand	964-969	6	49
β-strand	974-979	6	49
α-helix	987-990	4
β-strand	991	1	48
β-strand	992-998	7	49
β-strand	1007-1009	3	20
β-strand	1028-1030	3	20
β-strand	1037-1042	6	20
α-helix	1045-1061	17
α-helix	1070-1073	4
β-strand	1076-1078	3	50
β-strand	1081-1083	3	50
β-strand	1086	1	49
β-strand	1089-1090	2	20
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-25	5	1
β-strand	33-38	6	1
α-helix	39-40	2
β-strand	49-51	3	1
α-helix	60-62	3
β-strand	68	1	2
β-strand	75	1	3
β-strand	78	1	3
β-strand	83	1	2
β-strand	84	1	3
α-helix	87-90	4
α-helix	99-109	11
α-helix	121-129	9
α-helix	131-145	15

Chain e: 41 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	58-74	17
α-helix	77-79	3
α-helix	83-95	13
α-helix	99-121	23
α-helix	128-152	25
α-helix	154-156	3
α-helix	157-161	5
α-helix	162-163	2
α-helix	168-169	2
α-helix	170-178	9
α-helix	179-183	5
α-helix	186-204	19
α-helix	211-224	14
α-helix	226	1
α-helix	227-232	6
α-helix	233-251	19
α-helix	256-276	21
α-helix	280-282	3
α-helix	283-291	9
α-helix	292-296	5
α-helix	299-302	4
α-helix	303-307	5
α-helix	308-313	6
α-helix	316-326	11
α-helix	332-352	21
α-helix	355-357	3
α-helix	362-378	17
α-helix	384-398	15
α-helix	404-417	14
β-strand	418	1	51
α-helix	426-440	15
α-helix	446-462	17
β-strand	466	1	51
α-helix	469-487	19
α-helix	489-514	26
β-strand	522-529	8	6
α-helix	534-535	2
α-helix	545-561	17
β-strand	565-577	13	6
β-strand	580-583	4	52
β-strand	585-587	3	52
β-strand	588-592	5	6
α-helix	593-599	7
β-strand	607-609	3	53
α-helix	610-617	8
α-helix	621-632	12
β-strand	639-640	2	53
β-strand	653-656	4	53
β-strand	666-668	3	6
α-helix	693-707	15
β-strand	709-711	3	54
α-helix	712-722	11
α-helix	729-741	13
β-strand	745-747	3	54
β-strand	754-757	4	54

Chain N: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	4
β-strand	49	1	4
β-strand	55	1	5
α-helix	56-59	4
β-strand	67-71	5	4

Chain R: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	26-35	10	6
α-helix	52-53	2
α-helix	54-57	4
β-strand	70-72	3	7
β-strand	78-80	3	7
α-helix	81-90	10

Chain U: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	13-16	4	8
β-strand	22	1	9
α-helix	23-34	12
β-strand	41	1	10
β-strand	44	1	8
β-strand	49	1	8
β-strand	55	1	9
α-helix	56-59	4
β-strand	66-68	3	8
β-strand	71	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	D	protein	147	Homo sapiens	P62837 (AlphaFold model)
NEDD8	N	protein	76	Homo sapiens	Q15843 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	R	protein	108	Homo sapiens	P62877 (AlphaFold model)
Ubiquitin	U	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
DNA excision repair protein ERCC-8	a	protein	396	Homo sapiens	Q13216
DNA damage-binding protein 1	d	protein	1140	Homo sapiens	Q16531
Cullin-4A	e	protein	759	Homo sapiens	Q13619

Sequence of entity 1 (D), FASTA

>8B3I_1 Ubiquitin-conjugating enzyme E2 D2 (chains D)
MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 2 (N), FASTA

>8B3I_2 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Sequence of entity 3 (R), FASTA

>8B3I_3 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 4 (U), FASTA

>8B3I_4 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 5 (a), FASTA

>8B3I_5 DNA excision repair protein ERCC-8 (chains a)
MLGFLSARQTGLEDPLRLRRAESTRRVLGLELNKDRDVERIHGGGINTLDIEPVEGRYML
SGGSDGVIVLYDLENSSRQSYYTCKAVCSIGRDHPDVHRYSVETVQWYPHDTGMFTSSSF
DKTLKVWDTNTLQTADVFNFEETVYSHHMSPVSTKHCLVAVGTRGPKVQLCDLKSGSCSH
ILQGHRQEILAVSWSPRYDYILATASADSRVKLWDVRRASGCLITLDQHNGKKSQAVESA
NTAHNGKVNGLCFTSDGLHLLTVGTDNRMRLWNSSNGENTLVNYGKVCNNSKKGLKFTVS
CGCSSEFVFVPYGSTIAVYTVYSGEQITMLKGHYKTVDCCVFQSNFQELYSGSRDCNILA
WVPSLYEPVPDDDETTTKSQLNPAFEDAWSSSDEEG

Sequence of entity 6 (d), FASTA

>8B3I_6 DNA damage-binding protein 1 (chains d)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 7 (e), FASTA

>8B3I_7 Cullin-4A (chains e)
MADEAPRKGSFSALVGRTNGLTKPAALAAAPAKPGGAGGSKKLVIKNFRDRPRLPDNYTQ
DTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYKQLRQACEDHVQAQILP
FREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRT
HIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDLQVYKDSFELKFLEETN
CLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLT
AILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPEKDKD
MVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFINKRPNKPAELIAKHVDSKLRAG
NKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLK
HECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLTVNILTMGYWPTYTPME
VHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLL
MFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEF
KHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELY
NQLKFPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

C(N)RL4CSA-E2-Ub (state 2). Kokic, G., Cramer, P. To be published.

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
3L1Y 1.6 Å, Crystal structure of human UBC4 E2 conjugating enzyme
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub

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