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- PDB-5inc: Crystal structure of HLA-B5801, a protective HLA allele for HIV-1... -

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Basic information

Entry
Database: PDB / ID: 5inc
TitleCrystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection
Components
  • Beta-2-microglobulin
  • GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP
  • HLA class I histocompatibility antigen, B-58 alpha chain
KeywordsIMMUNE SYSTEM / HLA / HIV / QW9_S3T
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / regulation of natural killer cell mediated immunity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / regulation of natural killer cell mediated immunity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / viral budding via host ESCRT complex / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / protection from natural killer cell mediated cytotoxicity / TAP binding / Binding and entry of HIV virion / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / Membrane binding and targetting of GAG proteins / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / secretory granule membrane / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / Assembly Of The HIV Virion / positive regulation of T cell cytokine production / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / Budding and maturation of HIV virion / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / specific granule lumen / host multivesicular body / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell differentiation in thymus / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / negative regulation of neuron projection development / late endosome membrane / protein refolding / viral nucleocapsid / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / viral translational frameshifting / external side of plasma membrane / signaling receptor binding
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / MHC classes I/II-like antigen recognition protein / : / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag polyprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.881 Å
AuthorsLi, X. / Wang, J.-H.
Funding support United States, 1items
OrganizationGrant numberCountry
Ragon Institute of MGH, MIT and Harvard United States
CitationJournal: Protein Cell / Year: 2016
Title: Crystal structure of HLA-B*5801, a protective HLA allele for HIV-1 infection.
Authors: Li, X. / Lamothe, P.A. / Ng, R. / Xu, S. / Teng, M. / Walker, B.D. / Wang, J.H.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-58 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B-58 alpha chain
D: Beta-2-microglobulin
E: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP
F: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)89,6536
Polymers89,6536
Non-polymers00
Water28816
1
A: HLA class I histocompatibility antigen, B-58 alpha chain
B: Beta-2-microglobulin
E: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,8273
Polymers44,8273
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-17 kcal/mol
Surface area19510 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B-58 alpha chain
D: Beta-2-microglobulin
F: GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,8273
Polymers44,8273
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-15 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.397, 82.410, 154.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resseq 1:64 or resseq 66:78 or resseq...
21(chain C and (resseq 1:64 or resseq 66:78 or resseq...
12(chain B and (resseq 1:73 or resseq 75:99))
22(chain D and (resseq 1:73 or resseq 75:99))
13(chain F and (resseq 1:6 or resseq 8:9))
23(chain E and (resseq 1:6 or resseq 8:9))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:64 or resseq 66:78 or resseq...A1 - 64
121(chain A and (resseq 1:64 or resseq 66:78 or resseq...A66 - 78
131(chain A and (resseq 1:64 or resseq 66:78 or resseq...A80 - 120
141(chain A and (resseq 1:64 or resseq 66:78 or resseq...A122 - 127
151(chain A and (resseq 1:64 or resseq 66:78 or resseq...A129 - 193
161(chain A and (resseq 1:64 or resseq 66:78 or resseq...A195 - 277
211(chain C and (resseq 1:64 or resseq 66:78 or resseq...C1 - 64
221(chain C and (resseq 1:64 or resseq 66:78 or resseq...C66 - 78
231(chain C and (resseq 1:64 or resseq 66:78 or resseq...C80 - 120
241(chain C and (resseq 1:64 or resseq 66:78 or resseq...C122 - 127
251(chain C and (resseq 1:64 or resseq 66:78 or resseq...C129 - 193
261(chain C and (resseq 1:64 or resseq 66:78 or resseq...C195 - 277
112(chain B and (resseq 1:73 or resseq 75:99))B1 - 73
122(chain B and (resseq 1:73 or resseq 75:99))B75 - 99
212(chain D and (resseq 1:73 or resseq 75:99))D1 - 73
222(chain D and (resseq 1:73 or resseq 75:99))D75 - 99
113(chain F and (resseq 1:6 or resseq 8:9))F0
213(chain E and (resseq 1:6 or resseq 8:9))E0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein HLA class I histocompatibility antigen, B-58 alpha chain / Bw-58 / MHC class I antigen B*58


Mass: 31974.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10319, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP


Mass: 1104.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others) / References: UniProt: P04591*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIT REPRESENTS A NONSENSE MUTATION

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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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 291 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 18743 / % possible obs: 97.9 % / Redundancy: 10.1 % / Net I/σ(I): 9.06

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A1M

1a1m


Resolution: 2.881→43.697 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6
RfactorNum. reflection% reflection
Rfree0.2481 947 5.05 %
Rwork0.1949 --
obs0.1977 18738 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.68 Å2 / Biso mean: 36.792 Å2 / Biso min: 11.87 Å2
Refinement stepCycle: final / Resolution: 2.881→43.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 0 16 6334
Biso mean---30 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126511
X-RAY DIFFRACTIONf_angle_d1.2038847
X-RAY DIFFRACTIONf_chiral_restr0.063899
X-RAY DIFFRACTIONf_plane_restr0.0081168
X-RAY DIFFRACTIONf_dihedral_angle_d20.0993885
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2475X-RAY DIFFRACTION12.665TORSIONAL
12C2475X-RAY DIFFRACTION12.665TORSIONAL
21B941X-RAY DIFFRACTION12.665TORSIONAL
22D941X-RAY DIFFRACTION12.665TORSIONAL
31F59X-RAY DIFFRACTION12.665TORSIONAL
32E59X-RAY DIFFRACTION12.665TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.881-3.03290.3328860.23351934202071
3.0329-3.22280.30681180.23632310242885
3.2228-3.47160.28121350.22062445258089
3.4716-3.82080.25481300.20082663279397
3.8208-4.37320.26841530.174927492902100
4.3732-5.5080.19981580.167227882946100
5.508-43.70180.22791670.199329023069100

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