[English] 日本語
Yorodumi
- PDB-5ind: Crystal structure of HLA-B5801, a protective HLA allele for HIV-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ind
TitleCrystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection
Components
  • Beta-2-microglobulinBeta-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


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / 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 ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / 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 / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / TAP binding / Binding and entry of HIV virion / protection from natural killer cell mediated cytotoxicity / detection of bacterium / Membrane binding and targetting of GAG proteins / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / Budding and maturation of HIV virion / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi 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 / Beta-2-Microglobulin ...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) / MHC classes I/II-like antigen recognition protein / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIT REPRESENTS A NONSENSE MUTATION

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more