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- PDB-5vge: Crystal structure of HLA-C*07:02 in complex with RYR peptide -

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Basic information

Entry
Database: PDB / ID: 5vge
TitleCrystal structure of HLA-C*07:02 in complex with RYR peptide
Components
  • ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
  • Beta-2-microglobulinBeta-2 microglobulin
  • cDNA FLJ54183, highly similar to HLA class I histocompatibility antigen, Cw-7 alpha chain
KeywordsIMMUNE SYSTEM / Human leukocyte antigen Major histocompatibility complex Antigen presentation
Function / homology
Function and homology information


antigen processing and presentation / Chromatin modifying enzymes / epigenetic regulation of gene expression / TAP binding / 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 / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication ...antigen processing and presentation / Chromatin modifying enzymes / epigenetic regulation of gene expression / TAP binding / 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 / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / secretory granule membrane / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / PRC2 methylates histones and DNA / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Defective pyroptosis / HDACs deacetylate histones / lumenal side of endoplasmic reticulum membrane / RNA Polymerase I Promoter Escape / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of forebrain neuron differentiation / NoRC negatively regulates rRNA expression / ER to Golgi transport vesicle membrane / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / 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 / PKMTs methylate histone lysines / antigen processing and presentation of endogenous peptide antigen via MHC class I / RMTs methylate histone arginines / positive regulation of T cell cytokine production / Meiotic recombination / Pre-NOTCH Transcription and Translation / MHC class I protein complex / nucleosome assembly / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / nucleosome / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / positive regulation of protein binding / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / ER-Phagosome pathway / iron ion transport / Senescence-Associated Secretory Phenotype (SASP) / protein refolding
Similarity search - Function
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 / Histone H3 signature 1. / Histone H3 signature 2. / Beta-2-Microglobulin / Histone H3 ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Beta-2-Microglobulin / Histone H3 / MHC class I-like antigen recognition-like / Histone H3/CENP-A / MHC class I-like antigen recognition-like superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / MHC classes I/II-like antigen recognition protein / Histone-fold / 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
cDNA FLJ54183, highly similar to HLA class I histocompatibility antigen, Cw-7 alpha chain / HLA class I histocompatibility antigen, C alpha chain / Beta-2-microglobulin / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMobbs, J.I. / Vivian, J.P. / Gras, S. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and regulatory diversity shape HLA-C protein expression levels.
Authors: Kaur, G. / Gras, S. / Mobbs, J.I. / Vivian, J.P. / Cortes, A. / Barber, T. / Kuttikkatte, S.B. / Jensen, L.T. / Attfield, K.E. / Dendrou, C.A. / Carrington, M. / McVean, G. / Purcell, A.W. / ...Authors: Kaur, G. / Gras, S. / Mobbs, J.I. / Vivian, J.P. / Cortes, A. / Barber, T. / Kuttikkatte, S.B. / Jensen, L.T. / Attfield, K.E. / Dendrou, C.A. / Carrington, M. / McVean, G. / Purcell, A.W. / Rossjohn, J. / Fugger, L.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cDNA FLJ54183, highly similar to HLA class I histocompatibility antigen, Cw-7 alpha chain
B: Beta-2-microglobulin
C: ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7656
Polymers44,5683
Non-polymers1963
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-81 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.670, 99.670, 77.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein cDNA FLJ54183, highly similar to HLA class I histocompatibility antigen, Cw-7 alpha chain


Mass: 31654.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B4DVY0, UniProt: P10321*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide ARG-TYR-ARG-PRO-GLY-THR-VAL-ALA-LEU


Mass: 1034.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M HEPES pH 8.5 2 mM ZnSO4 28 % jeffamine ED-2001 (Hampton)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.68
11K, H, -L20.32
ReflectionResolution: 2.6→43.16 Å / Num. obs: 13655 / % possible obs: 100 % / Redundancy: 11.3 % / Rpim(I) all: 0.05 / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT6

4nt6


Resolution: 2.6→43.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.613 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22082 698 5.1 %RANDOM
Rwork0.1632 ---
obs0.16629 12942 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.984 Å2
Baniso -1Baniso -2Baniso -3
1--27.78 Å20 Å20 Å2
2---27.78 Å20 Å2
3---55.56 Å2
Refinement stepCycle: 1 / Resolution: 2.6→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 3 20 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193217
X-RAY DIFFRACTIONr_bond_other_d0.0020.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9394365
X-RAY DIFFRACTIONr_angle_other_deg0.94136526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52823.277177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9471533
X-RAY DIFFRACTIONr_chiral_restr0.0830.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1525.5711532
X-RAY DIFFRACTIONr_mcbond_other3.1455.571531
X-RAY DIFFRACTIONr_mcangle_it4.928.3541909
X-RAY DIFFRACTIONr_mcangle_other4.9188.3551910
X-RAY DIFFRACTIONr_scbond_it3.1755.7971685
X-RAY DIFFRACTIONr_scbond_other3.1755.7971685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0478.562456
X-RAY DIFFRACTIONr_long_range_B_refined7.51261.5773406
X-RAY DIFFRACTIONr_long_range_B_other7.51161.5883407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 39 -
Rwork0.25 960 -
obs--99.7 %

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