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- PDB-5v4m: Structure of HLA-DR15 with bound alpha3(135-145) peptide -

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Basic information

Entry
Database: PDB / ID: 5v4m
TitleStructure of HLA-DR15 with bound alpha3(135-145) peptide
Components
  • HLA-DRA1
  • alpha3(135-145)-HLA-DRB1*15:01
KeywordsIMMUNE SYSTEM / HLA-DR / immune complex / antigen presenation
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPetersen, J. / Rossjohn, J.
CitationJournal: Nature / Year: 2017
Title: Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells.
Authors: Ooi, J.D. / Petersen, J. / Tan, Y.H. / Huynh, M. / Willett, Z.J. / Ramarathinam, S.H. / Eggenhuizen, P.J. / Loh, K.L. / Watson, K.A. / Gan, P.Y. / Alikhan, M.A. / Dudek, N.L. / Handel, A. / ...Authors: Ooi, J.D. / Petersen, J. / Tan, Y.H. / Huynh, M. / Willett, Z.J. / Ramarathinam, S.H. / Eggenhuizen, P.J. / Loh, K.L. / Watson, K.A. / Gan, P.Y. / Alikhan, M.A. / Dudek, N.L. / Handel, A. / Hudson, B.G. / Fugger, L. / Power, D.A. / Holt, S.G. / Coates, P.T. / Gregersen, J.W. / Purcell, A.W. / Holdsworth, S.R. / La Gruta, N.L. / Reid, H.H. / Rossjohn, J. / Kitching, A.R.
History
DepositionMar 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HLA-DRA1
F: alpha3(135-145)-HLA-DRB1*15:01
A: HLA-DRA1
C: alpha3(135-145)-HLA-DRB1*15:01
G: HLA-DRA1
I: alpha3(135-145)-HLA-DRB1*15:01
J: HLA-DRA1
L: alpha3(135-145)-HLA-DRB1*15:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,01716
Polymers186,2568
Non-polymers2,7618
Water11,800655
1
D: HLA-DRA1
F: alpha3(135-145)-HLA-DRB1*15:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2994
Polymers46,5642
Non-polymers7352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-15 kcal/mol
Surface area18540 Å2
MethodPISA
2
A: HLA-DRA1
C: alpha3(135-145)-HLA-DRB1*15:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2104
Polymers46,5642
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-18 kcal/mol
Surface area18500 Å2
MethodPISA
3
G: HLA-DRA1
I: alpha3(135-145)-HLA-DRB1*15:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5024
Polymers46,5642
Non-polymers9382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-11 kcal/mol
Surface area18650 Å2
MethodPISA
4
J: HLA-DRA1
L: alpha3(135-145)-HLA-DRB1*15:01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0064
Polymers46,5642
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-21 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.590, 79.010, 95.821
Angle α, β, γ (deg.)87.64, 73.29, 89.97
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules DAGJFCIL

#1: Protein
HLA-DRA1 / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01903
#2: Protein
alpha3(135-145)-HLA-DRB1*15:01 / DW2.2/DR2.2 / MHC class II antigen DRB1*15 / DW2.2/DR2.2 / MHC class II antigen DRB1*15 / chimeric ...DW2.2/DR2.2 / MHC class II antigen DRB1*15 / DW2.2/DR2.2 / MHC class II antigen DRB1*15 / chimeric construct / DW2.2/DR2.2 / MHC class II antigen DRB1*15 / chimeric construct


Mass: 24644.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1, HLA-DRB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01911

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Sugars , 3 types, 8 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 513.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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Non-polymers , 1 types, 655 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2M KNO3 and 0.1M Bis-Tris-propane (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→50.35 Å / Num. obs: 106633 / % possible obs: 96.3 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.061 / Net I/av σ(I): 9.5 / Net I/σ(I): 41.65
Reflection shellRedundancy: 5.3 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 15528 / CC1/2: 0.692 / Rpim(I) all: 0.34 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.1→48.32 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.16
RfactorNum. reflection% reflection
Rfree0.244 3068 2.88 %
Rwork0.2167 --
obs0.2175 106601 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12464 0 180 655 13299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313108
X-RAY DIFFRACTIONf_angle_d0.66617886
X-RAY DIFFRACTIONf_dihedral_angle_d18.4117694
X-RAY DIFFRACTIONf_chiral_restr0.0451926
X-RAY DIFFRACTIONf_plane_restr0.0042314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13280.3171420.29064731X-RAY DIFFRACTION95
2.1328-2.16780.33581300.28114682X-RAY DIFFRACTION95
2.1678-2.20520.28961630.27264602X-RAY DIFFRACTION95
2.2052-2.24530.2941350.27294687X-RAY DIFFRACTION96
2.2453-2.28840.29141320.27644655X-RAY DIFFRACTION96
2.2884-2.33520.29121450.2654722X-RAY DIFFRACTION96
2.3352-2.38590.2791420.26214673X-RAY DIFFRACTION96
2.3859-2.44140.28791440.25724677X-RAY DIFFRACTION96
2.4414-2.50250.28791240.24884735X-RAY DIFFRACTION96
2.5025-2.57010.29281450.24664660X-RAY DIFFRACTION96
2.5701-2.64580.26881370.23524748X-RAY DIFFRACTION96
2.6458-2.73120.25221390.24334695X-RAY DIFFRACTION97
2.7312-2.82880.26651330.23094765X-RAY DIFFRACTION97
2.8288-2.9420.24261460.23554703X-RAY DIFFRACTION97
2.942-3.07590.22761260.2324745X-RAY DIFFRACTION97
3.0759-3.2380.27931450.21754700X-RAY DIFFRACTION97
3.238-3.44080.24041360.20834710X-RAY DIFFRACTION97
3.4408-3.70640.20421420.19434748X-RAY DIFFRACTION97
3.7064-4.07920.22981430.1854702X-RAY DIFFRACTION97
4.0792-4.66910.21131430.16414758X-RAY DIFFRACTION97
4.6691-5.88090.17471440.17124734X-RAY DIFFRACTION97
5.8809-48.33080.22341320.20514701X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -1.6102 Å / Origin y: -11.8697 Å / Origin z: -38.9284 Å
111213212223313233
T0.1693 Å2-0.0125 Å20.0021 Å2-0.2453 Å2-0.0005 Å2--0.2149 Å2
L0.0383 °20.0024 °20.0176 °2-0.1739 °20.0108 °2--0.1535 °2
S0.0111 Å °-0.0066 Å °-0.0066 Å °-0.007 Å °-0.0418 Å °0.0095 Å °0.0161 Å °-0.0013 Å °0.0303 Å °
Refinement TLS groupSelection details: all

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