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- PDB-3dcg: Crystal Structure of the HIV Vif BC-box in Complex with Human Elo... -

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Basic information

Entry
Database: PDB / ID: 3dcg
TitleCrystal Structure of the HIV Vif BC-box in Complex with Human ElonginB and ElonginC
Components
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
  • Virion infectivity factor
KeywordsLIGASE/VIRAL PROTEIN / HIV / Vif / AIDS / Host-virus interaction / Membrane / Phosphoprotein / RNA-binding / Ubl conjugation pathway / Virion / Nucleus / Transcription / Transcription regulation / LIGASE-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript ...target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / viral life cycle / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / virion component / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / host cell cytoplasm / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / RNA binding / nucleoplasm / membrane / cytosol
Similarity search - Function
Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family ...Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) protein / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Virion infectivity factor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStanley, B.J. / Ehrlich, E.S. / Short, L. / Yu, Y. / Xiao, Z. / Yu, X.-F. / Xiong, Y.
CitationJournal: J.Virol. / Year: 2008
Title: Structural insight into the human immunodeficiency virus Vif SOCS box and its role in human E3 ubiquitin ligase assembly
Authors: Stanley, B.J. / Ehrlich, E.S. / Short, L. / Yu, Y. / Xiao, Z. / Yu, X.-F. / Xiong, Y.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
C: Transcription elongation factor B polypeptide 2
D: Transcription elongation factor B polypeptide 1
E: Virion infectivity factor
F: Virion infectivity factor


Theoretical massNumber of molelcules
Total (without water)57,1416
Polymers57,1416
Non-polymers00
Water2,702150
1
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
F: Virion infectivity factor


Theoretical massNumber of molelcules
Total (without water)28,5713
Polymers28,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-27 kcal/mol
Surface area10170 Å2
MethodPISA
2
C: Transcription elongation factor B polypeptide 2
D: Transcription elongation factor B polypeptide 1
E: Virion infectivity factor


Theoretical massNumber of molelcules
Total (without water)28,5713
Polymers28,5713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.514, 66.913, 122.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETARGARGAA1 - 801 - 80
211METMETARGARGCC1 - 801 - 80
121PHEPHEGLUGLUAA85 - 9885 - 98
221PHEPHEGLUGLUCC85 - 9885 - 98
112METMETLEULEUBB17 - 462 - 31
212METMETLEULEUDD17 - 462 - 31
122GLUGLUTYRTYRBB59 - 8344 - 68
222GLUGLUTYRTYRDD59 - 8344 - 68
132GLUGLUCYSCYSBB89 - 11274 - 97
232GLUGLUCYSCYSDD89 - 11274 - 97
142LEULEUASNASNBB46 - 5831 - 43
242SERSERASNASNDD47 - 5832 - 43
113ASNASNLYSLYSEE140 - 1553 - 18
213ASNASNLYSLYSFF140 - 1553 - 18

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Transcription elongation factor B polypeptide 2 / ElonginB / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Elongin-B / EloB / ...ElonginB / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Elongin-B / EloB / Elongin 18 kDa subunit


Mass: 13147.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ElonginB / Plasmid: pACYCDUET-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15370
#2: Protein Transcription elongation factor B polypeptide 1 / ElonginC / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin-C / EloC / ...ElonginC / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin-C / EloC / Elongin 15 kDa subunit


Mass: 10974.616 Da / Num. of mol.: 2 / Fragment: UNP residues 17-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ElonginC / Plasmid: pACYCDUET-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15369
#3: Protein/peptide Virion infectivity factor / Vif / SOR protein / Virion infectivity factor p17 / Virion infectivity factor p7


Mass: 4448.283 Da / Num. of mol.: 2 / Fragment: UNP residues 139-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Strain: HXB3 / Gene: Virion Infectivity Factor / Plasmid: pETDUET-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12504
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris HCl pH 7.0, 40% PEG 350 MME, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2008
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→29.37 Å / Num. obs: 18219 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 11.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1762 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1vcb

1vcb


Resolution: 2.4→29.37 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.777 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.414 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23228 895 4.9 %RANDOM
Rwork0.18603 ---
obs0.18826 17246 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.74 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 150 3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223211
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.9894331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84923.824136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1315579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1821520
X-RAY DIFFRACTIONr_chiral_restr0.070.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21386
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22159
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.942046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55663229
X-RAY DIFFRACTIONr_scbond_it3.04861283
X-RAY DIFFRACTIONr_scangle_it4.48591102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A747LOOSE POSITIONAL0.375
1A747LOOSE THERMAL2.110
2B647LOOSE POSITIONAL0.425
2B647LOOSE THERMAL1.5810
3E119LOOSE POSITIONAL0.585
3E119LOOSE THERMAL1.3310
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 65 -
Rwork0.192 1216 -
obs--96.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.35270.2471-0.52682.8224-1.16865.8068-0.02080.0490.0357-0.0717-0.0102-0.1326-0.02970.30980.031-0.1976-0.0117-0.0055-0.12480.0133-0.072523.3977.0642.059
23.7510.0055-1.21643.8927-0.68446.0630.0395-0.15650.08210.2402-0.1023-0.10460.01410.30210.0628-0.14720.0004-0.0341-0.03320.0266-0.154521.0622.28521.962
33.12630.7147-1.91472.0978-0.85024.9249-0.1841-0.1041-0.30530.0109-0.05060.00540.71210.08570.23470.0001-0.0290.0299-0.1252-0.0051-0.023614.704-10.8660.2
43.1242-0.2621-0.27683.7505-0.78456.8736-0.12670.1471-0.1258-0.10940.09490.1460.4068-0.19490.0319-0.055-0.02370.0154-0.0712-0.0557-0.136315.656-5.614-19.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 981 - 98
2X-RAY DIFFRACTION2BB17 - 1122 - 97
3X-RAY DIFFRACTION2FF140 - 1553 - 18
4X-RAY DIFFRACTION3CC1 - 981 - 98
5X-RAY DIFFRACTION4DD17 - 1122 - 97
6X-RAY DIFFRACTION4EE140 - 1563 - 19

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