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- PDB-4p6z: Crystal structure of the human BST2 cytoplasmic domain and the HI... -

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Entry
Database: PDB / ID: 4p6z
TitleCrystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core
Components
  • (AP-1 complex subunit ...) x 4
  • Bone marrow stromal antigen 2
  • Protein Vpu
KeywordsPROTEIN TRANSPORT / BST2 / tetherin / Vpu / HIV / clathrin / AP1 / antiviral / restriction factor / antagonism
Function / homology
Function and homology information


negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / Lysosome Vesicle Biogenesis / endosome to melanosome transport / AP-1 adaptor complex / response to interferon-alpha / platelet dense granule organization / metalloendopeptidase inhibitor activity ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / Lysosome Vesicle Biogenesis / endosome to melanosome transport / AP-1 adaptor complex / response to interferon-alpha / platelet dense granule organization / metalloendopeptidase inhibitor activity / melanosome assembly / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / receptor catabolic process / positive regulation of leukocyte proliferation / MHC class II antigen presentation / CD4 receptor binding / determination of left/right symmetry / clathrin-coated vesicle / azurophil granule membrane / clathrin binding / negative regulation of viral genome replication / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / B cell activation / viral release from host cell / host cell membrane / response to type II interferon / monoatomic cation channel activity / side of membrane / vesicle-mediated transport / multivesicular body / clathrin-coated pit / Neutrophil degranulation / MHC class II antigen presentation / receptor-mediated endocytosis / cytoplasmic vesicle membrane / negative regulation of cell migration / Nef mediated downregulation of MHC class I complex cell surface expression / trans-Golgi network membrane / regulation of actin cytoskeleton organization / intracellular protein transport / kidney development / trans-Golgi network / negative regulation of cell growth / response to virus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / synaptic vesicle / presynapse / heart development / defense response to virus / symbiont-mediated-mediated suppression of host tetherin activity / early endosome / positive regulation of canonical NF-kappaB signal transduction / symbiont-mediated suppression of host innate immune response / apical plasma membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / Golgi membrane / innate immune response / lysosomal membrane / intracellular membrane-bounded organelle / synapse / Neutrophil degranulation / lipid binding / protein kinase binding / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Vpu protein / Vpu protein cytoplasmic domain superfamily / Vpu protein / Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / Beta-Lactamase - #60 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. ...Vpu protein / Vpu protein cytoplasmic domain superfamily / Vpu protein / Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / Beta-Lactamase - #60 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein Vpu / AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / AP-1 complex subunit sigma-1A / AP-1 complex subunit beta-1 / Bone marrow stromal antigen 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsJia, X. / Xiong, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI102778 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097064 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081668 United States
The James B. Pendleton Charitable Trust United States
CitationJournal: Elife / Year: 2014
Title: Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1.
Authors: Jia, X. / Weber, E. / Tokarev, A. / Lewinski, M. / Rizk, M. / Suarez, M. / Guatelli, J. / Xiong, Y.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: AP-1 complex subunit gamma-1
S: AP-1 complex subunit sigma-1A
M: AP-1 complex subunit mu-1
B: AP-1 complex subunit beta-1
V: Protein Vpu
T: Bone marrow stromal antigen 2


Theoretical massNumber of molelcules
Total (without water)216,0546
Polymers216,0546
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20470 Å2
ΔGint-91 kcal/mol
Surface area70930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.536, 160.536, 118.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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AP-1 complex subunit ... , 4 types, 4 molecules GSMB

#1: Protein AP-1 complex subunit gamma-1 / Adapter-related protein complex 1 subunit gamma-1 / Adaptor protein complex AP-1 subunit gamma-1 / ...Adapter-related protein complex 1 subunit gamma-1 / Adaptor protein complex AP-1 subunit gamma-1 / Clathrin assembly protein complex 1 gamma-1 large chain / Gamma-adaptin / Gamma1-adaptin / Golgi adaptor HA1/AP1 adaptin subunit gamma-1


Mass: 70944.023 Da / Num. of mol.: 1
Fragment: BST2/tetheirn cytoplasmic domain, UNP residues 1-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22892
#2: Protein AP-1 complex subunit sigma-1A / Adapter-related protein complex 1 subunit sigma-1A / Adaptor protein complex AP-1 subunit sigma-1A ...Adapter-related protein complex 1 subunit sigma-1A / Adaptor protein complex AP-1 subunit sigma-1A / Clathrin assembly protein complex 1 sigma-1A small chain / Clathrin coat assembly protein AP19 / Golgi adaptor HA1/AP1 adaptin sigma-1A subunit / HA1 19 kDa subunit / Sigma 1a subunit of AP-1 clathrin / Sigma-adaptin 1A / Sigma1A-adaptin


Mass: 18787.059 Da / Num. of mol.: 1 / Fragment: HIV-1 Vpu cytoplasmic domain / Mutation: Q11R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S1, AP19, CLAPS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61966
#3: Protein AP-1 complex subunit mu-1 / AP-mu chain family member mu1A / Adapter-related protein complex 1 subunit mu-1 / Adaptor protein ...AP-mu chain family member mu1A / Adapter-related protein complex 1 subunit mu-1 / Adaptor protein complex AP-1 subunit mu-1 / Clathrin assembly protein complex 1 mu-1 medium chain 1 / Clathrin coat assembly protein AP47 / Clathrin coat-associated protein AP47 / Golgi adaptor HA1/AP1 adaptin mu-1 subunit / Mu-adaptin 1 / Mu1A-adaptin


Mass: 48606.730 Da / Num. of mol.: 1
Fragment: Clathrin adaptor protein complex 1 (AP1) core, UNP residues 1-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35585
#4: Protein AP-1 complex subunit beta-1 / Adapter-related protein complex 1 subunit beta-1 / Adaptor protein complex AP-1 subunit beta-1 / ...Adapter-related protein complex 1 subunit beta-1 / Adaptor protein complex AP-1 subunit beta-1 / Beta-1-adaptin / Beta-adaptin 1 / Clathrin assembly protein complex 1 beta large chain / Golgi adaptor HA1/AP1 adaptin beta subunit


Mass: 67770.258 Da / Num. of mol.: 1 / Fragment: UNP residues 1-584 / Mutation: T431A, E476K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1B1, ADTB1, BAM22, CLAPB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10567

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Protein / Protein/peptide / Non-polymers , 3 types, 16 molecules VT

#5: Protein Protein Vpu / U ORF protein / Viral protein U


Mass: 7123.607 Da / Num. of mol.: 1 / Fragment: UNP residues 21-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate SF162 / Gene: vpu / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19554
#6: Protein/peptide Bone marrow stromal antigen 2 / BST-2 / HM1.24 antigen / Tetherin


Mass: 2822.180 Da / Num. of mol.: 1 / Fragment: UNP residues 1-21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10589
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: Peg 6000, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 59937 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 30.036 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.988 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3036 5.1 %RANDOM
Rwork0.1858 56901 --
obs0.188 59937 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK
Displacement parametersBiso max: 261.61 Å2 / Biso mean: 107.107 Å2 / Biso min: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.93 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13918 0 0 14 13932
Biso mean---74.22 -
Num. residues----1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01914161
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9819133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.40151735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77724.385634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.102152689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0671595
X-RAY DIFFRACTIONr_chiral_restr0.0850.22217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110383
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 243 -
Rwork0.34 4174 -
all-4417 -
obs--99.57 %
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)
11.02210.32310.26762.0537-0.21780.94090.02580.39530.604-0.7715-0.1598-0.5112-0.23110.22910.13410.850.11870.29620.65570.27420.6438-56.38-24.4236.086
23.33780.13250.35025.859-0.1233.92570.40250.43170.3179-0.963-0.3479-0.4847-0.16480.0247-0.05460.72070.19120.12790.35820.08830.076-69.694-41.4453.589
32.25170.7017-0.12330.78450.29821.10890.1242-0.02340.0521-0.1501-0.29510.1018-0.06760.11830.17080.69110.0501-0.01020.5857-0.00670.3647-82.609-35.18844.571
42.1556-0.4536-1.10182.21761.33583.04180.1897-0.4646-0.21640.4328-0.1312-0.22550.01930.2493-0.05850.458-0.1103-0.12760.3690.13610.0801-64.02-56.54658.008
52.60540.1999-0.54111.7233-0.12881.32470.1739-0.01250.68960.0859-0.268-0.1441-0.28360.2050.09410.6323-0.0793-0.05010.34120.02920.2821-64.657-25.42847.896
61.1665.2857-4.337124.2106-19.866416.3021-0.23430.16840.2965-0.92031.13571.12110.746-0.9143-0.90131.12630.1418-0.19190.6601-0.19890.3482-84.626-43.5778.582
79.81731.46813.7190.48-2.612543.9357-0.5281-0.6711-1.6725-0.0729-0.0479-0.28641.2059-0.10440.5761.01920.0320.15220.6330.27750.6053-74.933-65.47169.746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G2 - 588
2X-RAY DIFFRACTION2S1 - 147
3X-RAY DIFFRACTION3M2 - 135
4X-RAY DIFFRACTION4M158 - 423
5X-RAY DIFFRACTION5B14 - 583
6X-RAY DIFFRACTION6V61 - 67
7X-RAY DIFFRACTION7T6 - 12

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