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- PDB-4mcz: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4mcz
TitleImmune Receptor
Components
  • Citrullinated Vimentin
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
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 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 / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / 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 / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / positive regulation of collagen biosynthetic process / Co-inhibition by PD-1 / epidermis development / Caspase-mediated cleavage of cytoskeletal proteins / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / phagocytic vesicle / regulation of mRNA stability / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / negative regulation of inflammatory response to antigenic stimulus / peptide antigen assembly with MHC class II protein complex / clathrin-coated endocytic vesicle membrane / MHC class II protein complex / Late endosomal microautophagy / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / structural constituent of cytoskeleton / positive regulation of immune response / cellular response to type II interferon / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / nuclear matrix / Chaperone Mediated Autophagy / Aggrephagy / neuron projection development / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / peroxisome / double-stranded RNA binding / T cell receptor signaling pathway / negative regulation of neuron projection development / early endosome membrane / cellular response to lipopolysaccharide / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / lysosome / positive regulation of viral entry into host cell / cytoskeleton / immune response / protein domain specific binding / axon / Golgi membrane / lysosomal membrane / external side of plasma 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: 2.41 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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 2.0Nov 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 2.1Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,2466
Polymers46,5833
Non-polymers6643
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-24 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.110, 183.430, 77.280
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-664-

HOH

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Components

#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
#3: Protein/peptide Citrullinated Vimentin


Mass: 1438.634 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
Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#4: 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.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.97 %
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: Feb 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.41→48.84 Å / Num. obs: 18843 / Redundancy: 4.7 % / Rmerge(I) obs: 0.158
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3 / % possible all: 100

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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: 2.41→48.84 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 20.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 969 5.14 %
Rwork0.1887 --
obs0.1908 18841 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 42 239 3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033285
X-RAY DIFFRACTIONf_angle_d1.024466
X-RAY DIFFRACTIONf_dihedral_angle_d14.3381204
X-RAY DIFFRACTIONf_chiral_restr0.065479
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.53710.24661230.21282524X-RAY DIFFRACTION100
2.5371-2.6960.24411570.21992504X-RAY DIFFRACTION100
2.696-2.90420.27281450.21462515X-RAY DIFFRACTION100
2.9042-3.19640.26441310.20572546X-RAY DIFFRACTION100
3.1964-3.65880.21081480.17832529X-RAY DIFFRACTION100
3.6588-4.60910.18451360.15732570X-RAY DIFFRACTION100
4.6091-48.85150.24451290.18392684X-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)
12.22390.0512-0.8732.9698-0.8830.9318-0.0335-0.288-0.18860.3934-0.0381-0.0479-0.0278-0.01110.06040.1503-0.0082-0.01090.15140.00470.104141.320224.394-0.0499
21.6971-0.90520.33992.8282-0.97273.2858-0.2111-0.6998-0.78580.78850.20010.17630.4757-0.0861-0.15830.3810.09920.04430.29930.15480.368842.493412.38556.7608
31.5637-0.45270.25395.4319-3.39214.4860.2368-0.18860.0540.358-0.0876-0.0367-0.34470.43550.01140.1376-0.0364-0.01860.2187-0.05780.10251.627135.8123-4.7135
42.03870.54330.09030.73720.38830.48730.026-0.08960.27330.07740.1385-0.0696-0.28470.0585-0.08920.1391-0.008-0.02890.06440.04060.10537.944444.2823-10.1702
52.23380.43830.14923.2439-0.36451.756-0.2671-0.3119-0.54210.1875-0.2120.36710.3719-0.34270.13160.2848-0.00220.32880.1883-0.01540.230114.372721.42685.6496
61.03930.0694-0.38380.53740.09630.1571-0.2019-0.2317-0.07730.36070.09650.0368-0.14970.00250.01110.31110.05840.0930.22520.00920.105324.033831.84636.1698
71.78490.3254-1.06220.8039-1.0911.6635-0.0827-0.0821-0.07720.13760.0723-0.06330.38460.00920.01250.15940.0094-0.01840.1471-0.0070.100930.035127.6829-1.2439
81.1484-0.1004-0.32071.3544-0.39781.68280.1486-0.27790.26260.52840.04040.7104-0.3520.0797-0.23060.2950.05230.20720.2733-0.04320.278114.3831.42779.9108
90.8328-0.2614-1.15343.9208-2.1613.22410.33790.40320.8280.29120.4750.976-0.2463-0.4626-0.32630.23540.05560.01430.1204-0.03940.272617.765436.70931.597
102.1532-0.2211-0.56321.97780.15591.225-0.07470.0167-0.1919-0.07720.0589-0.1729-0.02240.05560.03310.09360.0136-0.00880.1067-0.02430.101348.501924.8223-13.7143
112.94580.06451.05231.2868-0.17251.0562-0.0721-0.2827-0.5785-0.08690.12380.19030.0299-0.2505-0.05690.14960.03020.06010.1520.08860.30111.74110.8999-6.9124
124.51262.8323-1.55151.8358-1.40384.16310.457-0.21090.424-0.01360.06340.2152-0.71990.4265-0.14340.2411-0.02550.04560.1468-0.01420.236653.720226.0256-6.5433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 153 )
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 166 )
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 181 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 190 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 13 )

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