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- PDB-4mdj: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4mdj
TitleImmune Receptor
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Vimentin
KeywordsIMMUNE SYSTEM / HLA-DR / Antigen presentation / T-cell receptor / Membrane
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / cellular response to muramyl dipeptide ...keratin filament binding / lens fiber cell development / intermediate filament organization / regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / cellular response to muramyl dipeptide / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / structural constituent of eye lens / MHC class II receptor activity / positive regulation of T cell mediated immune response to tumor cell / positive regulation of CD4-positive, alpha-beta T cell activation / astrocyte development / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / Striated Muscle Contraction / microtubule organizing center / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / intermediate filament / polysaccharide binding / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cell leading edge / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Bergmann glial cell differentiation / macrophage differentiation / negative regulation of type II interferon production / humoral immune response / Generation of second messenger molecules / immunological synapse / positive regulation of collagen biosynthetic process / PD-1 signaling / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / phagocytic vesicle / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / protein tetramerization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cellular response to type II interferon / cognition / peptide antigen assembly with MHC class II protein complex / nuclear matrix / MHC class II protein complex / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / neuron projection development / positive regulation of T cell activation / double-stranded RNA binding / negative regulation of neuron projection development / peroxisome / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / scaffold protein binding / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / cytoskeleton / immune response / positive regulation of protein phosphorylation / protein domain specific binding / Golgi membrane / axon / external side of plasma membrane / lysosomal membrane / focal adhesion
Similarity search - Function
Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Intermediate filament head, DNA-binding domain / : / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament 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 / Vimentin / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsScally, S.W. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2013
Title: A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis.
Authors: Scally, S.W. / Petersen, J. / Law, S.C. / Dudek, N.L. / Nel, H.J. / Loh, K.L. / Wijeyewickrema, L.C. / Eckle, S.B. / van Heemst, J. / Pike, R.N. / McCluskey, J. / Toes, R.E. / La Gruta, N.L. ...Authors: Scally, S.W. / Petersen, J. / Law, S.C. / Dudek, N.L. / Nel, H.J. / Loh, K.L. / Wijeyewickrema, L.C. / Eckle, S.B. / van Heemst, J. / Pike, R.N. / McCluskey, J. / Toes, R.E. / La Gruta, N.L. / Purcell, A.W. / Reid, H.H. / Thomas, R. / Rossjohn, J.
History
DepositionAug 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
C: Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4897
Polymers46,5603
Non-polymers9294
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-32 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.442, 182.445, 77.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-807-

HOH

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 1 / Fragment: Extracellular Domain, UNP residues 26-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR-4 / DR4


Mass: 23253.588 Da / Num. of mol.: 1 / Fragment: Extracellular Domain, UNP residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P13760, UniProt: P01911*PLUS

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Vimentin


Mass: 1386.625 Da / Num. of mol.: 1 / Fragment: Residues 66-78 / Source method: obtained synthetically / Details: This sequence is from human vimentin / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670

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Sugars , 2 types, 3 molecules

#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.: 1
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-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.: 2
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 , 2 types, 536 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 25% PEG 3350, 0.2M Potassium Nitrate, 0.1M Bis-Tris-Propane pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→62.43 Å / Num. obs: 52300 / Redundancy: 6.4 % / Rmerge(I) obs: 0.105
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.611 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 2640 5.05 %
Rwork0.1621 --
obs0.1635 52276 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 60 535 3746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053408
X-RAY DIFFRACTIONf_angle_d1.0574659
X-RAY DIFFRACTIONf_dihedral_angle_d16.4811281
X-RAY DIFFRACTIONf_chiral_restr0.076505
X-RAY DIFFRACTIONf_plane_restr0.005610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.27361360.22462597X-RAY DIFFRACTION100
1.7309-1.76420.25311530.20992548X-RAY DIFFRACTION100
1.7642-1.80020.22981360.19822606X-RAY DIFFRACTION100
1.8002-1.83940.2251380.18482549X-RAY DIFFRACTION100
1.8394-1.88220.21531360.17852581X-RAY DIFFRACTION100
1.8822-1.92920.22691270.16842604X-RAY DIFFRACTION100
1.9292-1.98140.20171220.17232601X-RAY DIFFRACTION100
1.9814-2.03970.20251520.16622588X-RAY DIFFRACTION100
2.0397-2.10550.1821400.15392583X-RAY DIFFRACTION100
2.1055-2.18080.21431280.15652613X-RAY DIFFRACTION100
2.1808-2.26810.18391330.15462595X-RAY DIFFRACTION100
2.2681-2.37130.18451350.15972620X-RAY DIFFRACTION100
2.3713-2.49630.21541290.16172604X-RAY DIFFRACTION100
2.4963-2.65270.17781390.16142613X-RAY DIFFRACTION100
2.6527-2.85750.19621430.16672616X-RAY DIFFRACTION100
2.8575-3.1450.17971570.16752624X-RAY DIFFRACTION100
3.145-3.59990.18491380.14882642X-RAY DIFFRACTION100
3.5999-4.53490.14211460.13672665X-RAY DIFFRACTION100
4.5349-45.62770.1731520.16542787X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.62520.20420.90317.780.11570.7105-0.0411-0.19770.12570.2758-0.0028-0.1068-0.0411-0.00380.03330.06550.00170.00710.1053-0.01490.0638-40.9813-26.6376-3.7663
22.6021-0.3402-0.16994.25750.35524.01650.0852-0.58740.34340.5043-0.05930.2187-0.1725-0.00780.00410.13910.008-0.00190.1851-0.06410.1295-40.2287-18.29785.9769
32.3576-0.0368-0.1636.29853.25943.95270.0031-0.1528-0.08670.3096-0.08340.37990.3174-0.34230.09740.0865-0.02220.02130.13840.05370.1266-50.7871-35.8908-3.9729
43.7812.17691.90222.5961.15061.7041-0.21340.07020.13960.03380.1098-0.0871-0.12530.20480.06110.12270.0116-0.02380.10020.01210.0766-23.0184-29.7276-0.911
52.9978-0.30441.6230.62220.34421.3349-0.0946-0.3483-0.00350.25020.0588-0.0847-0.0543-0.17890.03650.14980.0101-0.01820.11960.00940.0722-26.789-31.87993.7293
64.13961.25422.78342.72611.323.23520.05620.0033-0.23360.24470.0701-0.49050.0610.1626-0.12590.13840.002-0.02990.11770.03150.1202-17.8655-31.93784.699
71.4707-0.00810.29592.0112-0.13461.2939-0.02570.06520.1672-0.1346-0.0631-0.1254-0.02670.05520.07850.0773-0.00140.00590.06830.01840.079-44.637-27.3312-14.2081
83.13521.11021.20082.70091.52032.3874-0.085-0.05860.2444-0.062-0.01720.12050.0208-0.13740.10020.09460.00440.00680.07180.02960.098-53.0863-21.4171-12.7163
94.01160.3401-1.31171.15430.35061.0002-0.0467-0.22520.081-0.02540.1178-0.01950.1150.1629-0.07850.13320.0162-0.04890.1303-0.04920.1446-12.4464-11.5677-5.7105
101.7444-0.2318-0.79180.69230.04361.12040.0361-0.09110.3127-0.04850.0524-0.147-0.05220.1747-0.07310.0942-0.0061-0.01710.1191-0.03560.1738-9.9783-9.3567-8.619
113.25210.24150.66912.04861.60423.99310.0773-0.22960.18050.1419-0.15350.24560.1219-0.30640.12950.0822-0.00790.01590.14670.00670.1294-53.408-25.0001-5.4303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 89 )
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 133 )
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 192 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 13 )

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