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

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Basic information

Entry
Database: PDB / ID: 5ind
TitleCrystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection
Components
  • Beta-2-microglobulin
  • GLN-ALA-SER-GLN-ASP-VAL-LYS-ASN-TRP
  • HLA class I histocompatibility antigen, B-58 alpha chain
KeywordsIMMUNE SYSTEM / HLA / HIV / QW9_E5D
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 / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis ...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 / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / Binding and entry of HIV virion / detection of bacterium / Membrane binding and targetting of GAG proteins / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / Assembly Of The HIV Virion / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / defense response / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / Budding and maturation of HIV virion / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / host multivesicular body / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / viral translational frameshifting / innate immune response / lysosomal membrane
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 / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / : / 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: 2.132 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 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

Downloads & links

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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-SER-GLN-ASP-VAL-LYS-ASN-TRP
F: GLN-ALA-SER-GLN-ASP-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)89,5976
Polymers89,5976
Non-polymers00
Water7,476415
1
A: HLA class I histocompatibility antigen, B-58 alpha chain
B: Beta-2-microglobulin
E: GLN-ALA-SER-GLN-ASP-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,7993
Polymers44,7993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-20 kcal/mol
Surface area19270 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B-58 alpha chain
D: Beta-2-microglobulin
F: GLN-ALA-SER-GLN-ASP-VAL-LYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,7993
Polymers44,7993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-18 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.413, 82.280, 157.720
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
11(chain B and (resseq 1:2 or resseq 4:6 or (resid...
21(chain D and (resseq 1:2 or resseq 4:6 or (resid...
12(chain A and (resseq 1:74 or resseq 76:94 or (resid...
22(chain C and (resseq 1:74 or resseq 76:94 or (resid...
13chain F
23chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEGLNGLN(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 21 - 2
121THRTHRLYSLYS(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB4 - 64 - 6
131ILEILEILEILE(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB77
141ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
151ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
161ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
171ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
181ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
191ILEILEMETMET(chain B and (resseq 1:2 or resseq 4:6 or (resid...BB1 - 991 - 99
211ILEILEGLNGLN(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 21 - 2
221THRTHRLYSLYS(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD4 - 64 - 6
231ILEILEILEILE(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD77
241ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
251ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
261ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
271ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
281ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
291ILEILEMETMET(chain D and (resseq 1:2 or resseq 4:6 or (resid...DD1 - 991 - 99
112GLYGLYTYRTYR(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 741 - 74
122GLUGLUILEILE(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA76 - 9476 - 94
132ILEILEILEILE(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA9595
142GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
152GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
162GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
172GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
182GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
192GLYGLYHISHIS(chain A and (resseq 1:74 or resseq 76:94 or (resid...AA1 - 2771 - 277
212GLYGLYTYRTYR(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 741 - 74
222GLUGLUILEILE(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC76 - 9476 - 94
232ILEILEILEILE(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC9595
242GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
252GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
262GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
272GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
282GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
292GLYGLYHISHIS(chain C and (resseq 1:74 or resseq 76:94 or (resid...CC1 - 2771 - 277
113GLNGLNTRPTRPchain FFF1 - 91 - 9
213GLNGLNTRPTRPchain EEE1 - 91 - 9

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-SER-GLN-ASP-VAL-LYS-ASN-TRP


Mass: 1076.139 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.: 415 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 15% PEG4K, 20% 2-proponal / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 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: 2.11→50 Å / Num. obs: 50306 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 23.99

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Processing

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

1a1m


Resolution: 2.132→44.302 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.2291 2402 4.78 %
Rwork0.1865 --
obs0.1885 50296 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.71 Å2 / Biso mean: 35.537 Å2 / Biso min: 13.32 Å2
Refinement stepCycle: final / Resolution: 2.132→44.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6317 0 0 415 6732
Biso mean---39.94 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096516
X-RAY DIFFRACTIONf_angle_d1.078856
X-RAY DIFFRACTIONf_chiral_restr0.058899
X-RAY DIFFRACTIONf_plane_restr0.0071171
X-RAY DIFFRACTIONf_dihedral_angle_d16.6183888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B882X-RAY DIFFRACTION6.24TORSIONAL
12D882X-RAY DIFFRACTION6.24TORSIONAL
21A2518X-RAY DIFFRACTION6.24TORSIONAL
22C2518X-RAY DIFFRACTION6.24TORSIONAL
31F70X-RAY DIFFRACTION6.24TORSIONAL
32E70X-RAY DIFFRACTION6.24TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1324-2.17590.31071130.21882010212371
2.1759-2.22320.27191410.225728212962100
2.2232-2.27490.2721430.2228032946100
2.2749-2.33180.30581290.216628692998100
2.3318-2.39480.26561390.215428242963100
2.3948-2.46530.28881520.202528102962100
2.4653-2.54490.26811460.202728372983100
2.5449-2.63580.23811320.204828462978100
2.6358-2.74130.24461490.202828472996100
2.7413-2.86610.21841420.20328452987100
2.8661-3.01710.23361530.207728613014100
3.0171-3.20610.25331340.197328472981100
3.2061-3.45360.24931240.192529133037100
3.4536-3.8010.20221380.174128663004100
3.801-4.35060.20341470.157129303077100
4.3506-5.47960.18511470.149229223069100
5.4796-44.31150.21071730.18683043321699

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