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- PDB-4md5: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4md5
TitleImmune Receptor
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Citrullinated Vimentin
KeywordsIMMUNE SYSTEM / HLA-DR / Antigen presentation / T-cell receptor / Citrullination / Membrane
Function / homology
Function and homology information


lens fiber cell development / keratin filament binding / 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 / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation ...lens fiber cell development / keratin filament binding / 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 / positive regulation of T cell mediated immune response to tumor cell / 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 / MHC class II receptor activity / structural constituent of eye lens / 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 monocyte differentiation / CD4 receptor binding / Striated Muscle Contraction / inflammatory response to antigenic stimulus / positive regulation of kinase activity / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / cell leading edge / 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 / Bergmann glial cell differentiation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / positive regulation of collagen biosynthetic process / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / regulation of mRNA stability / MHC class II antigen presentation / phagocytic vesicle / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / nuclear matrix / cellular response to type II interferon / Aggrephagy / peptide antigen assembly with MHC class II protein complex / Chaperone Mediated Autophagy / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peroxisome / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / neuron projection development / Interferon gamma signaling / positive regulation of immune response / double-stranded RNA binding / Downstream TCR signaling / positive regulation of T cell activation / negative regulation of neuron projection development / 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 viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / cytoskeleton / positive regulation of protein phosphorylation / immune response / protein domain specific binding / lysosomal membrane / external side of plasma membrane / axon / Golgi 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 / 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
TRIETHYLENE GLYCOL / 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: 1.65 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 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Dec 27, 2023Group: Derived calculations / Category: struct_conn

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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: Citrullinated Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,11415
Polymers46,6013
Non-polymers1,51412
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-8 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.420, 183.001, 77.516
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-447-

HOH

21B-490-

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: 23294.709 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 Citrullinated Vimentin


Mass: 1386.602 Da / Num. of mol.: 1 / Fragment: Residues 66-78 / Source method: obtained synthetically
Details: This sequence is from human vimentin and contains citrulline at position 71
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 , 3 types, 475 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 26% 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→45.75 Å / Num. obs: 58009 / Redundancy: 7.2 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.166 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 2908 5.02 %
Rwork0.1626 --
obs0.1637 57973 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→32.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 98 466 3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053512
X-RAY DIFFRACTIONf_angle_d1.0224790
X-RAY DIFFRACTIONf_dihedral_angle_d16.2741323
X-RAY DIFFRACTIONf_chiral_restr0.073517
X-RAY DIFFRACTIONf_plane_restr0.005627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67710.21141390.19362573X-RAY DIFFRACTION100
1.6771-1.7060.20961560.18932579X-RAY DIFFRACTION100
1.706-1.7370.23321170.18132593X-RAY DIFFRACTION100
1.737-1.77040.22891420.18062613X-RAY DIFFRACTION100
1.7704-1.80650.1951420.17322590X-RAY DIFFRACTION100
1.8065-1.84580.18841390.17012593X-RAY DIFFRACTION100
1.8458-1.88870.23321380.16992591X-RAY DIFFRACTION100
1.8887-1.9360.231410.16422594X-RAY DIFFRACTION100
1.936-1.98830.16191380.15442619X-RAY DIFFRACTION100
1.9883-2.04680.20211180.15162604X-RAY DIFFRACTION100
2.0468-2.11290.17711360.15562616X-RAY DIFFRACTION100
2.1129-2.18840.18671260.15682604X-RAY DIFFRACTION100
2.1884-2.27590.18211360.15472634X-RAY DIFFRACTION100
2.2759-2.37950.16681300.16682624X-RAY DIFFRACTION100
2.3795-2.50490.20391300.16572630X-RAY DIFFRACTION100
2.5049-2.66180.19061400.16842621X-RAY DIFFRACTION100
2.6618-2.86720.19231510.17532635X-RAY DIFFRACTION100
2.8672-3.15550.22751510.17182626X-RAY DIFFRACTION100
3.1555-3.61160.17071400.15682661X-RAY DIFFRACTION100
3.6116-4.54810.15061470.14322676X-RAY DIFFRACTION100
4.5481-32.17210.16751510.16492789X-RAY DIFFRACTION99
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)
12.1335-0.1817-0.85654.8211-0.16660.8722-0.0821-0.2048-0.13290.24920.07650.0350.02030.03030.05270.08540.0127-0.0120.11260.01240.03641.701726.3749-4.1731
22.4589-0.2859-0.05062.3202-0.85943.5281-0.0095-0.7324-0.46590.50220.0222-0.17790.07110.03550.01520.22330.0272-0.00270.24520.09430.142241.109218.27726.1038
32.75340.07810.35464.812-1.67843.39690.0067-0.20770.13290.4023-0.0064-0.4131-0.28320.2450.05180.0993-0.0151-0.0260.1269-0.05670.126751.791436.2469-4.3418
43.87992.0502-1.75922.7435-0.90311.7146-0.17790.0476-0.1320.17330.11760.19170.0957-0.2220.0330.14940.02280.0370.09810.00270.083523.862529.6415-0.6676
52.1397-0.0798-1.39960.5105-0.3031.4548-0.06-0.3285-0.03420.30350.04720.084-0.02040.23250.07680.19150.03220.02820.14010.0060.073327.625632.09973.8314
62.49290.5733-1.76092.3569-0.68682.69980.011-0.12540.21240.29580.09030.5248-0.0296-0.12-0.1120.18360.02740.05850.1217-00.129119.454932.38274.374
71.8008-0.065-0.51731.7259-0.1121.1205-0.0792-0.0046-0.2111-0.10460.0109-0.11320.04160.07580.05160.07490.0006-0.00210.0754-0.01720.088948.826724.6646-13.5928
82.5631-0.07141.25971.6117-0.19431.3814-0.0572-0.2221-0.5053-0.02770.17110.3194-0.0647-0.2357-0.08990.14130.01070.0630.14680.08610.289111.877410.9141-6.7206
92.69081.8473-1.6564.0539-4.49615.03250.1098-0.303-0.19880.4134-0.2499-0.3274-0.13570.3470.15770.10060.0184-0.02440.15310.01490.130654.287925.3681-5.8802
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 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 90 through 191 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 13 )

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