4N9F | pdb_00004n9f

Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex

PDB DOI: https://doi.org/10.2210/pdb4N9F/pdb

Classification: LIGASE/VIRAL PROTEIN
Organism(s): Homo sapiens, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-21 Released: 2014-01-08
Deposition Author(s): Guo, Y.Y., Dong, L.Y., Huang, Z.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.324 (Depositor), 0.327 (DCC)
R-Value Work:
0.262 (Depositor), 0.266 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for hijacking CBF-b and CUL5 E3 ligase complex by HIV-1 Vif

Guo, Y.Y., Dong, L.Y., Qiu, X.L., Wang, Y.S., Zhang, B.L., Liu, H.N., Yu, Y., Zang, Y., Yang, M.J., Huang, Z.W.

(2014) Nature 505: 229-233

Macromolecule Content

Total Structure Weight: 1,200.46 kDa
Atom Count: 77,274
Modeled Residue Count: 9,494
Deposited Residue Count: 10,260
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-5	A [auth U] DB [auth w] EA [auth l] F [auth C] JA [auth r] A [auth U], DB [auth w], EA [auth l], F [auth C], JA [auth r], K [auth I], OA [auth x], P [auth O], TA [auth 3], U [auth V], YA [auth 9], Z [auth f]	311	Homo sapiens	Mutation(s): 0 Gene Names: CUL5, VACM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q93034 (Homo sapiens) Explore Q93034 Go to UniProtKB: Q93034
PHAROS: Q93034 GTEx: ENSG00000166266
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93034
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 1	AA [auth h] B [auth Y] EB [auth B] FA [auth n] G [auth E] AA [auth h], B [auth Y], EB [auth B], FA [auth n], G [auth E], KA [auth t], L [auth K], PA [auth z], Q, UA [auth 5], V [auth Z], ZA [auth T]	96	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 2	AB [auth e] BA [auth g] C [auth X] FB [auth H] GA [auth m] AB [auth e], BA [auth g], C [auth X], FB [auth H], GA [auth m], H [auth D], LA [auth s], M [auth J], QA [auth y], R [auth P], VA [auth 4], W	102	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Core-binding factor subunit beta	BB [auth k] CA [auth i] D [auth a] GB [auth N] HA [auth o] BB [auth k], CA [auth i], D [auth a], GB [auth N], HA [auth o], I [auth F], MA [auth u], N [auth L], RA [auth 0], S [auth R], WA [auth 6], X [auth c]	170	Homo sapiens	Mutation(s): 0 Gene Names: CBFB, CBFbeta
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens) Explore Q13951 Go to UniProtKB: Q13951
PHAROS: Q13951 GTEx: ENSG00000067955
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13951
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion infectivity factor	CB [auth q] DA [auth j] E [auth b] HB [auth 2] IA [auth p] CB [auth q], DA [auth j], E [auth b], HB [auth 2], IA [auth p], J [auth G], NA [auth v], O [auth M], SA [auth 1], T [auth S], XA [auth 7], Y [auth d]	176	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: vif
UniProt
Find proteins for P12504 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12504 Go to UniProtKB: P12504
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12504
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain IB [auth b] SDF format, chain JB [auth G] SDF format, chain KB [auth M] SDF format, chain LB [auth S] SDF format, chain MB [auth d] SDF format, chain NB [auth j] SDF format, chain OB [auth p] SDF format, chain PB [auth v] SDF format, chain QB [auth 1] SDF format, chain RB [auth 7] SDF format, chain SB [auth q] SDF format, chain TB [auth 2] MOL2 format, chain IB [auth b] MOL2 format, chain JB [auth G] MOL2 format, chain KB [auth M] MOL2 format, chain LB [auth S] MOL2 format, chain MB [auth d] MOL2 format, chain NB [auth j] MOL2 format, chain OB [auth p] MOL2 format, chain PB [auth v] MOL2 format, chain QB [auth 1] MOL2 format, chain RB [auth 7] MOL2 format, chain SB [auth q] MOL2 format, chain TB [auth 2] mmCIF format, chain IB [auth b] mmCIF format, chain JB [auth G] mmCIF format, chain KB [auth M] mmCIF format, chain LB [auth S] mmCIF format, chain MB [auth d] mmCIF format, chain NB [auth j] mmCIF format, chain OB [auth p] mmCIF format, chain PB [auth v] mmCIF format, chain QB [auth 1] mmCIF format, chain RB [auth 7] mmCIF format, chain SB [auth q] mmCIF format, chain TB [auth 2]	IB [auth b] JB [auth G] KB [auth M] LB [auth S] MB [auth d] IB [auth b], JB [auth G], KB [auth M], LB [auth S], MB [auth d], NB [auth j], OB [auth p], PB [auth v], QB [auth 1], RB [auth 7], SB [auth q], TB [auth 2]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IB [auth b] Focus chain JB [auth G] Focus chain KB [auth M] Focus chain LB [auth S] Focus chain MB [auth d] Focus chain NB [auth j] Focus chain OB [auth p] Focus chain PB [auth v] Focus chain QB [auth 1] Focus chain RB [auth 7] Focus chain SB [auth q] Focus chain TB [auth 2] Interactions & Density Focus chain IB [auth b] Focus chain JB [auth G] Focus chain KB [auth M] Focus chain LB [auth S] Focus chain MB [auth d] Focus chain NB [auth j] Focus chain OB [auth p] Focus chain PB [auth v] Focus chain QB [auth 1] Focus chain RB [auth 7] Focus chain SB [auth q] Focus chain TB [auth 2]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.324 (Depositor), 0.327 (DCC)
R-Value Work: 0.262 (Depositor), 0.266 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.925	α = 65.51
b = 204.002	β = 90.28
c = 247.866	γ = 90.5

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-08

Deposition Author(s):

Guo, Y.Y.

Dong, L.Y.

Huang, Z.W.

Revision History (Full details and data files)

Version 1.0: 2014-01-08
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

4N9F | pdb_00004n9f

Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex

Literature

Structural basis for hijacking CBF-b and CUL5 E3 ligase complex by HIV-1 Vif

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Biological Assembly 9

Biological Assembly 10

Biological Assembly 11

Biological Assembly 12

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)