[English] 日本語
Yorodumi
- PDB-3wuw: KIR3DL1 in complex with HLA-B*57:01.I80T -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wuw
TitleKIR3DL1 in complex with HLA-B*57:01.I80T
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • Killer cell immunoglobulin-like receptor 3DL1
  • Peptide
KeywordsPROTEIN BINDING / Immune receptor complex
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / natural killer cell mediated cytotoxicity / immunoglobulin mediated immune response / TAP binding / protection from natural killer cell mediated cytotoxicity / FCGR activation / 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 / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / detection of bacterium / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / secretory granule membrane / Regulation of Complement cascade / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / Endosomal/Vacuolar pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / 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 / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / Regulation of actin dynamics for phagocytic cup formation / 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 / FCERI mediated NF-kB activation / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / early endosome membrane / blood microparticle / amyloid fibril formation / Potential therapeutics for SARS / protein homotetramerization / molecular adaptor activity / intracellular iron ion homeostasis
Similarity search - Function
: / Immunoglobulin / Immunoglobulin 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 ...: / Immunoglobulin / Immunoglobulin 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 / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Immunoglobulin kappa constant / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVivian, J.P. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2014
Title: Mutational and structural analysis of KIR3DL1 reveals a lineage-defining allotypic dimorphism that impacts both HLA and peptide sensitivity
Authors: O'connor, G.M. / Vivian, J.P. / Widjaja, J.M. / Bridgeman, J.S. / Gostick, E. / Lafont, B.A.P. / Anderson, S.K. / Price, D.A. / Brooks, A.G. / Rossjohn, J. / Mcvicar, D.W.
History
DepositionMay 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: Peptide
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4067
Polymers77,7424
Non-polymers6643
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-23 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.058, 61.494, 66.356
Angle α, β, γ (deg.)94.66, 99.58, 109.14
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 3 types, 3 molecules ABG

#1: Protein HLA class I histocompatibility antigen, B-57 alpha chain / Bw-57 / MHC class I antigen B*57


Mass: 31627.004 Da / Num. of mol.: 1
Fragment: HLA-B*57:01 extracellular domain, UNP residues 25-299
Mutation: I80T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-B*57:01, HLAB / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11635.002 Da / Num. of mol.: 1 / Fragment: Beta 2 Microglobulin, UNP residues 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, Beta 2 Microglobulin, CDABP0092, HDCMA22P / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK ...CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 33513.816 Da / Num. of mol.: 1
Fragment: KIR3DL1*001 extracellular domains, UNP residues 28-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD158E, KIR3DL1, KIR3DL1*001, NKAT3, NKB1 / Plasmid: pHLSec / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P43629

-
Protein/peptide / Sugars / Non-polymers , 3 types, 497 molecules C

#3: Protein/peptide Peptide


Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesised peptide / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01834*PLUS
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE ENTITY3 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE ...THE SEQUENCE OF THE ENTITY3 OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG3350, 2% tacsimate(pH 5.0), 0.1M tri-sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9546 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9546 Å / Relative weight: 1
ReflectionResolution: 2→46.472 Å / Num. obs: 49831 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7177 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2→40 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2388 2528 5.08 %
Rwork0.1984 --
obs0.2005 49812 97.22 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.656 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9561 Å2-5.7528 Å2-7.0117 Å2
2---2.6459 Å26.863 Å2
3---3.602 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 42 493 5860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085538
X-RAY DIFFRACTIONf_angle_d1.2937516
X-RAY DIFFRACTIONf_dihedral_angle_d13.2892048
X-RAY DIFFRACTIONf_chiral_restr0.085780
X-RAY DIFFRACTIONf_plane_restr0.007983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03850.28931240.2569214780
2.0385-2.08010.29411550.2528262597
2.0801-2.12530.27361320.243261198
2.1253-2.17480.30761360.2278264197
2.1748-2.22920.26341430.2278262397
2.2292-2.28940.2811490.2231268598
2.2894-2.35680.30081510.2116262998
2.3568-2.43290.24161440.215262298
2.4329-2.51980.27221410.2151262198
2.5198-2.62070.26181270.223268498
2.6207-2.740.26831410.2226267398
2.74-2.88440.25231250.2154270599
2.8844-3.06510.26191340.2147265398
3.0651-3.30170.22641490.2032265699
3.3017-3.63380.22841360.1876268399
3.6338-4.15940.21591360.1655267599
4.1594-5.23920.19671430.15268199
5.2392-46.48450.21121620.1999267099

+
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