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- PDB-4md0: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4md0
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


keratin filament binding / lens fiber cell development / regulation of interleukin-4 production / intermediate filament organization / 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 / regulation of interleukin-4 production / intermediate filament organization / 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 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 T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament cytoskeleton / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / 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 / microtubule organizing center / Bergmann glial cell differentiation / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / positive regulation of collagen biosynthetic process / immunological synapse / Co-inhibition by PD-1 / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / detection of bacterium / T cell receptor binding / phagocytic vesicle / negative regulation of T cell proliferation / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / Late endosomal microautophagy / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / positive regulation of T cell activation / cognition / nuclear matrix / Chaperone Mediated Autophagy / Interferon gamma signaling / Aggrephagy / neuron projection development / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / peroxisome / Downstream TCR signaling / double-stranded RNA binding / T cell receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of neuron projection development / cellular response to lipopolysaccharide / early endosome membrane / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / molecular adaptor activity / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / immune response / protein domain specific binding / axon / Golgi membrane / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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: 2.194 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _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_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 / pdbx_validate_rmsd_angle / 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
Revision 3.2Nov 20, 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: Citrullinated Vimentin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4506
Polymers46,5833
Non-polymers8673
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-19 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.127, 183.413, 77.312
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-701-

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: 23224.617 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 / Non-polymers , 2 types, 355 molecules C

#3: Protein/peptide Citrullinated Vimentin


Mass: 1438.588 Da / Num. of mol.: 1 / Fragment: Residues 59-71 / Source method: obtained synthetically
Details: This sequence is from human vimentin and contains citrulline at position 64,69 and 71
Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 24% 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.95369
Australian Synchrotron MX22
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 25, 2012
2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.19→91.26 Å / Num. obs: 23984 / Redundancy: 4.6 % / Rmerge(I) obs: 0.155
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.6 / % possible all: 98.3

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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: 2.194→39.438 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 1164 5.02 %
Rwork0.1742 --
obs0.1759 23207 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→39.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 56 354 3549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053354
X-RAY DIFFRACTIONf_angle_d1.2124563
X-RAY DIFFRACTIONf_dihedral_angle_d14.6891237
X-RAY DIFFRACTIONf_chiral_restr0.051490
X-RAY DIFFRACTIONf_plane_restr0.005594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29420.26241520.22442747X-RAY DIFFRACTION95
2.2942-2.41510.26741150.21032820X-RAY DIFFRACTION96
2.4151-2.56640.23141550.20412806X-RAY DIFFRACTION96
2.5664-2.76450.2481450.1972795X-RAY DIFFRACTION96
2.7645-3.04260.22621580.18212744X-RAY DIFFRACTION94
3.0426-3.48270.20981590.16562729X-RAY DIFFRACTION93
3.4827-4.38690.16651550.14332693X-RAY DIFFRACTION91
4.3869-39.44480.17121250.15662709X-RAY DIFFRACTION87
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)
11.1824-0.052-0.44032.8098-0.33210.4986-0.0807-0.0881-0.00970.15940.04020.1021-0.0776-0.00920.02920.09650.0212-0.00640.1295-0.01050.081641.831226.5059-4.0986
22.1894-0.16060.57831.094-0.09431.6579-0.0242-0.6031-0.2940.4449-0.007-0.02890.03950.07980.04860.23410.0218-0.01180.22050.07610.165741.322418.56075.7517
31.4367-0.37040.18463.2531-2.22363.65840.0891-0.15860.02270.0742-0.0327-0.3018-0.15250.2172-0.02830.1328-0.0172-0.01310.1753-0.07270.135151.686835.7673-4.758
42.3131.2326-0.87661.6892-0.40610.9101-0.3788-0.2622-0.08850.11880.06860.0262-0.1315-0.18990.05020.0970.06920.1220.19080.00620.043524.525631.4244-1.5207
50.78130.4023-0.30170.9346-0.2540.4051-0.068-0.0989-0.1605-0.03030.23020.33370.0163-0.0819-0.02960.02810.14680.37040.1306-0.0925-0.542924.663131.36693.1035
60.7971-0.0534-0.13160.4558-0.13180.0818-0.1077-0.2118-0.06470.22790.0860.09190.01440.08310.01430.16150.02450.04390.09840.00780.046727.284528.64583.48
72.26751.371-0.48763.4318-0.93561.95970.1415-0.40550.12220.4021-0.09090.4251-0.13680.0475-0.09780.25770.01990.14820.1708-0.02320.199114.528432.27219.3974
84.21782.3875-1.88732.8578-1.4221.68760.17210.33110.294-0.02440.24460.6237-0.1684-0.3728-0.19560.20820.0840.00570.1666-0.00860.244917.902336.69441.4208
91.14620.1496-0.22941.0942-0.00580.9198-0.06220.0446-0.1071-0.12240.0381-0.1167-0.01920.03580.0170.08190.00970.00780.0958-0.02530.089748.851225.711-14.2972
103.07770.10290.56250.6032-0.13461.1477-0.0074-0.2566-0.1284-0.11070.04680.0368-0.0661-0.2282-0.00860.17460.03040.07540.15380.05880.222914.601311.9652-5.0025
111.2964-0.3340.38530.3049-0.04620.5456-0.1021-0.0845-0.4359-0.07280.13090.2291-0.0282-0.0752-0.02870.1440.01410.03830.15190.0630.298710.90939.8377-8.1341
121.41411.4599-0.70985.794-2.4792.49230.1136-0.1322-0.006-0.01040.0394-0.1671-0.05410.0302-0.13370.1613-0.0460.03430.1610.01510.178952.910525.0366-6.2279
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 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 154 )
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 166 )
8X-RAY DIFFRACTION8chain 'A' and (resid 167 through 181 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 133 )
11X-RAY DIFFRACTION11chain 'B' and (resid 134 through 190 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 12 )

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