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- PDB-4md4: Immune Receptor -

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Basic information

Entry
Database: PDB / ID: 4md4
TitleImmune Receptor
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Aggrecan core protein
KeywordsIMMUNE SYSTEM / HLA-DR / Antigen presentation / T-cell receptor / Citrullination / Membrane
Function / homology
Function and homology information


Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / chondrocyte development / proteoglycan biosynthetic process / hyaluronic acid binding ...Defective CHST6 causes MCDC1 / Defective ST3GAL3 causes MCT12 and EIEE15 / keratan sulfate catabolic process / keratan sulfate biosynthetic process / Keratan sulfate degradation / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / Keratan sulfate biosynthesis / chondrocyte development / proteoglycan biosynthetic process / hyaluronic acid binding / 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 / collagen fibril organization / intermediate filament / transport vesicle membrane / extracellular matrix structural constituent / T-helper 1 type immune response / polysaccharide binding / cartilage condensation / 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 / Generation of second messenger molecules / negative regulation of type II interferon production / immunological synapse / basement membrane / PD-1 signaling / ECM proteoglycans / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / Degradation of the extracellular matrix / T cell receptor binding / extracellular matrix organization / lysosomal lumen / extracellular matrix / trans-Golgi network membrane / central nervous system development / skeletal system development / 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 / Golgi lumen / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / heart development / T cell receptor signaling pathway / early endosome membrane / carbohydrate binding / collagen-containing extracellular matrix / 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 / cell adhesion / 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 / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Aggrecan/versican, C-type lectin-like domain / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / 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 ...Aggrecan/versican, C-type lectin-like domain / Link domain / Extracellular link domain / Link domain signature. / Link domain profile. / Link (Hyaluronan-binding) / 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 / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / HLA class II histocompatibility antigen, DRB1 beta chain / Aggrecan core protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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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: Aggrecan core protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0009
Polymers46,9473
Non-polymers1,0536
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-23 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.091, 182.580, 77.539
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-741-

HOH

21B-785-

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 , 1 types, 1 molecules C

#3: Protein/peptide Aggrecan core protein / Cartilage-specific proteoglycan core protein / CSPCP / Chondroitin sulfate proteoglycan core ...Cartilage-specific proteoglycan core protein / CSPCP / Chondroitin sulfate proteoglycan core protein 1 / Chondroitin sulfate proteoglycan 1 / Aggrecan core protein 2


Mass: 1802.916 Da / Num. of mol.: 1 / Fragment: UNP residues 89-103 / Source method: obtained synthetically
Details: This sequence is from human aggrecan and contains citrulline at positions 93 and 95
Source: (synth.) Homo sapiens (human) / References: UniProt: P16112

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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 / N-Acetylglucosamine


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, 473 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
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: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.95→62.97 Å / Num. obs: 34301 / Redundancy: 6.5 % / Rmerge(I) obs: 0.122
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.6 / % possible all: 85.8

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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: 1.95→45.077 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1718 5.01 %
Rwork0.1647 --
obs0.167 34283 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→45.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 68 470 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063355
X-RAY DIFFRACTIONf_angle_d1.1064555
X-RAY DIFFRACTIONf_dihedral_angle_d15.21226
X-RAY DIFFRACTIONf_chiral_restr0.076489
X-RAY DIFFRACTIONf_plane_restr0.004592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00740.3125950.24022285X-RAY DIFFRACTION82
2.0074-2.07220.24411250.212473X-RAY DIFFRACTION90
2.0722-2.14620.24121380.18332669X-RAY DIFFRACTION97
2.1462-2.23220.2181350.17022776X-RAY DIFFRACTION100
2.2322-2.33380.22911650.16362725X-RAY DIFFRACTION100
2.3338-2.45680.2091470.16832742X-RAY DIFFRACTION100
2.4568-2.61070.23591360.17632794X-RAY DIFFRACTION100
2.6107-2.81230.26431440.18012764X-RAY DIFFRACTION100
2.8123-3.09520.23091540.17722788X-RAY DIFFRACTION100
3.0952-3.54290.18631720.15692784X-RAY DIFFRACTION100
3.5429-4.46310.17281550.13192827X-RAY DIFFRACTION100
4.4631-45.08870.17131520.14572938X-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)
12.0711-0.2577-0.58625.6113-0.07480.3589-0.1585-0.1848-0.05830.10280.21280.1287-0.03840.0650.00540.07450.0026-0.0010.12650.00930.058941.721626.5723-3.902
22.2973-0.2425-0.45072.6572-1.05942.127-0.0248-1.0589-0.37780.6526-0.0067-0.2732-0.0767-0.1553-0.01520.18580.0049-0.01410.27930.12870.173641.257118.55625.8582
31.76580.54770.00341.8707-0.30730.6662-0.0834-0.08330.10470.00790.0666-0.2776-0.11530.1610.01030.1379-0.0122-0.00450.132-0.06340.071546.686238.5161-6.3218
43.21620.3628-1.09323.2415-0.41542.924-0.281-0.234-0.5099-0.17460.18310.54940.5614-0.14470.17250.18840.00180.06390.25320.03520.201714.268421.41795.0246
52.26681.2438-0.93481.7404-0.7260.6929-0.1405-0.112-0.13050.11530.1024-0.01770.0689-0.09940.02820.10790.03360.01870.12290.01240.066424.521931.14483.1396
61.3419-0.1275-0.44561.1693-0.65750.7387-0.1234-0.2287-0.11150.19150.1150.04410.06270.08580.03620.14890.02340.01050.15980.00140.054327.163728.46463.4843
72.44130.2571-0.08923.1025-0.47922.23790.0662-0.81130.2650.62230.19230.6481-0.4771-0.1080.07910.22580.02390.18370.2233-0.04160.154914.328431.84229.4265
85.23933.4225-2.66825.8879-1.91812.65870.12250.33580.75710.12410.32391.126-0.1546-0.3794-0.25810.16140.0387-0.00470.16170.00490.160815.763634.67691.5805
92.1110.3177-0.90881.4869-0.20431.1-0.0503-0.0048-0.1072-0.0721-0.019-0.0002-0.0010.01570.07560.07120.0078-0.02180.0732-0.01910.047645.183327.1721-14.4037
103.1487-4.9969-0.78358.20991.00880.88770.17730.38140.2346-0.2656-0.1469-0.2882-0.19370.1470.01840.1124-0.02340.01310.1554-0.00440.109256.124933.9445-19.1177
111.85420.2524-0.31841.3674-0.20651.4529-0.0857-0.0409-0.67480.0429-0.0361-0.07220.00190.01860.06230.09730.04540.03330.08870.01690.230851.679414.5725-9.8725
123.43610.37341.04051.13250.1830.4679-0.0618-0.3826-0.3035-0.15710.07520.028-0.0327-0.1675-0.02430.13740.02360.05820.14210.06990.178612.704812.3132-5.3275
131.7197-0.8120.48510.789-0.12211.1895-0.0431-0.098-0.5871-0.02230.11970.26660.066-0.1572-0.05290.1237-0.00710.03640.11880.07640.28510.96839.7255-8.3423
143.18081.7561-1.80256.7662-4.14095.2281-0.0273-0.3294-0.45920.3971-0.4437-0.7433-0.16480.44870.41740.11340.006-0.03080.19670.03030.169953.265122.6946-5.0523
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 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 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 184 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 89 )
12X-RAY DIFFRACTION12chain 'B' and (resid 90 through 133 )
13X-RAY DIFFRACTION13chain 'B' and (resid 134 through 190 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 13 )

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