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- PDB-4fqx: Crystal structure of HLA-DM bound to HLA-DR1 -

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Basic information

Entry
Database: PDB / ID: 4fqx
TitleCrystal structure of HLA-DM bound to HLA-DR1
Components
  • (HLA class II histocompatibility antigen, ...) x 4
  • Synthetic peptide
KeywordsIMMUNE SYSTEM / immune complex / peptide loading / peptide editing / antigen presentation
Function / homology
Function and homology information


MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity ...MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / 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 / 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 T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / 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 / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of T cell proliferation / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / early endosome membrane / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 ...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 / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DM alpha chain / HLA class II histocompatibility antigen, DM beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.599 Å
AuthorsSethi, D.K. / Pos, W. / Wucherpfennig, K.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Crystal Structure of the HLA-DM-HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection.
Authors: Pos, W. / Sethi, D.K. / Call, M.J. / Schulze, M.S. / Anders, A.K. / Pyrdol, J. / Wucherpfennig, K.W.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain
E: Synthetic peptide
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7046
Polymers92,2805
Non-polymers4241
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-68 kcal/mol
Surface area34790 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DM alpha chain
D: HLA class II histocompatibility antigen, DM beta chain


Theoretical massNumber of molelcules
Total (without water)45,2262
Polymers45,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-32 kcal/mol
Surface area19040 Å2
MethodPISA
3
E: Synthetic peptide
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4784
Polymers47,0543
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-27 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.190, 121.649, 138.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HLA class II histocompatibility antigen, ... , 4 types, 4 molecules CDAB

#1: Protein HLA class II histocompatibility antigen, DM alpha chain / MHC class II antigen DMA / Really interesting new gene 6 protein


Mass: 22992.891 Da / Num. of mol.: 1 / Fragment: unp residues 27-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: DM alpha chain, DMA, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, HLA-DMA, RING6
Plasmid: pEE14.1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Lec3.2.8.1 / References: UniProt: P28067
#2: Protein HLA class II histocompatibility antigen, DM beta chain / MHC class II antigen DMB / Really interesting new gene 7 protein


Mass: 22233.170 Da / Num. of mol.: 1 / Fragment: unp residues 19-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: DM beta chain, DMB, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, HLA-DMB, RING7
Plasmid: pEE14.1 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / References: UniProt: P28068
#4: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22111.936 Da / Num. of mol.: 1 / Fragment: unp residues 26-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HLA-DR1 alpha chain, HLA-DRA, HLA-DRA1, MHC CLASS II MOLECULE
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01903
#5: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 23735.449 Da / Num. of mol.: 1 / Fragment: unp residues 30-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: beta chain, HLA-DR1, HLA-DRB1, MHC CLASS II MOLECULE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide / Sugars / Non-polymers , 3 types, 126 molecules E

#3: Protein/peptide Synthetic peptide


Mass: 1206.478 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 34280 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.693.30.533195
2.69-2.83.40.387198.8
2.8-2.933.50.252198.6
2.93-3.083.50.178198.5
3.08-3.283.50.113198
3.28-3.533.40.071198.3
3.53-3.883.50.053197.6
3.88-4.453.40.041197.3
4.45-5.63.40.043196.5
5.6-503.30.034194.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→36.141 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 0 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1742 5.1 %
Rwork0.194 --
obs0.1964 34135 97.06 %
all-34135 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.9118 Å2
Refinement stepCycle: LAST / Resolution: 2.599→36.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 28 124 6196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096263
X-RAY DIFFRACTIONf_angle_d1.1888530
X-RAY DIFFRACTIONf_dihedral_angle_d15.9572252
X-RAY DIFFRACTIONf_chiral_restr0.079928
X-RAY DIFFRACTIONf_plane_restr0.0061109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5991-2.67560.3241240.26392509X-RAY DIFFRACTION92
2.6756-2.76190.33121540.2632691X-RAY DIFFRACTION98
2.7619-2.86060.33941540.26192674X-RAY DIFFRACTION99
2.8606-2.97510.33291420.26112712X-RAY DIFFRACTION98
2.9751-3.11040.3031440.25492700X-RAY DIFFRACTION98
3.1104-3.27430.28161440.23352714X-RAY DIFFRACTION98
3.2743-3.47930.25441390.20982748X-RAY DIFFRACTION98
3.4793-3.74770.24271400.19112696X-RAY DIFFRACTION98
3.7477-4.12430.24471420.17892720X-RAY DIFFRACTION98
4.1243-4.720.17971500.14552707X-RAY DIFFRACTION97
4.72-5.94240.19461660.15412717X-RAY DIFFRACTION96
5.9424-36.14480.21391430.18552805X-RAY DIFFRACTION94
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)
10.30780.2333-0.05880.2424-0.16370.4352-0.38990.14040.27820.0321-0.279-0.2093-0.9460.5463-0.3460.7234-0.6064-0.28110.39160.19570.5557-7.628.4382-12.9916
20.0175-0.0025-0.01240.00520.0055-0.00190.05510.1532-0.0389-0.01940.01520.02120.02910.10590.00260.4759-0.27020.07150.98780.02770.94460.2837-7.8231-27.2399
30.1097-0.07180.08040.07350.02240.3766-0.16940.26420.16870.027-0.1123-0.2596-0.49560.2481-0.20860.4184-0.136-0.00550.53260.1140.4144-9.6157-4.9859-23.9651
40.31370.103-0.20640.4312-0.2320.2542-0.33480.1020.25630.1428-0.06850.0595-0.8394-0.2896-0.16591.19660.0147-0.36210.10940.11290.538-20.152714.2929-13.2402
50.032-0.0496-0.03370.04530.04030.02090.1294-0.0058-0.0485-0.1113-0.20380.2393-0.24450.0920.00020.6531-0.0558-0.1470.46770.10890.5298-27.46933.6563-30.9583
60.5788-0.1952-0.44180.08370.15190.323-0.39240.3025-0.0355-0.0293-0.3865-0.0619-0.2515-0.5354-0.1850.9649-0.1889-0.28590.44450.19940.4366-30.662.0788-43.6638
70.00430.00010.00620.0149-0.00360.00750.187-0.05320.1357-0.0193-0.0328-0.0876-0.0283-0.09110.00060.5087-0.0387-0.03010.5078-0.10080.647-26.6457-11.648123.1359
80.0019-0.01240.00860.0434-0.0140.0886-0.1127-0.10490.0480.1202-0.0153-0.0043-0.26840.046700.2640.0074-0.02690.34350.00410.3424-23.3604-12.22092.4233
90.06910.0026-0.02280.02670.0180.02310.0491-0.14710.16050.0017-0.02320.1635-0.4029-0.0065-00.47030.0051-0.0550.4307-0.01490.3632-21.8755-9.408310.2287
100.17970.0538-0.01530.02990.03650.0451-0.0770.1986-0.0386-0.0425-0.0376-0.00870.06640.02860.00010.31180.0024-0.00580.34160.01540.3466-21.0661-26.934-6.9073
110.0606-0.06130.04320.0625-0.01160.06710.10080.2278-0.0013-0.0189-0.05550.0935-0.1125-0.102600.2496-0.0086-0.00910.33370.01320.3221-17.3665-22.5874-8.1483
120.07220.00570.02650.10590.00530.0129-0.07530.0891-0.19770.0752-0.1009-0.00540.30190.1355-0.00030.41120.0650.00690.42410.02450.4473-13.8362-31.3782-13.7832
130.0169-0.0218-0.01180.004-0.05110.04380.1264-0.00540.1471-0.1808-0.0320.06340.0864-0.11380.00030.21980.0607-0.02770.39270.04520.2835-21.041-25.036710.7711
140.13720.11840.06470.19890.03840.14190.1022-0.05360.19290.1788-0.0567-0.0772-0.1003-0.38490.00410.26530.13860.01880.4028-0.00150.3886-37.7612-12.481714.4692
150.26950.1834-0.16930.1374-0.11810.1088-0.14170.2438-0.0714-0.2025-0.0448-0.02760.0042-0.0974-0.01180.26240.0616-0.00350.22740.11270.5071-34.017-4.6354-12.0245
160.06790.00890.01740.082-0.07360.0611-0.2140.16020.11410.01030.16410.0296-0.1654-0.046600.254-0.0666-0.02570.30790.00850.2637-38.4544-23.537-26.0701
170.129-0.0556-0.08540.1088-0.04540.0781-0.0297-0.04190.0473-0.27840.0948-0.18560.08530.064400.4172-0.0449-0.00520.3090.0170.3803-33.9992-24.8818-23.477
180.0103-0.00040.03250.0415-0.02510.0386-0.18420.44430.1161-0.2934-0.04450.13030.0918-0.099200.4012-0.0083-0.04980.47360.06560.4154-39.5034-17.5744-30.1457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 15:137 )C15 - 137
2X-RAY DIFFRACTION2( CHAIN C AND RESID 138:147 )C138 - 147
3X-RAY DIFFRACTION3( CHAIN C AND RESID 148:200 )C148 - 200
4X-RAY DIFFRACTION4( CHAIN D AND RESID 3:133 )D3 - 133
5X-RAY DIFFRACTION5( CHAIN D AND RESID 134:157 )D134 - 157
6X-RAY DIFFRACTION6( CHAIN D AND RESID 158:193 )D158 - 193
7X-RAY DIFFRACTION7( CHAIN E AND RESID 87:93 )E87 - 93
8X-RAY DIFFRACTION8( CHAIN A AND RESID 2:45 )A2 - 45
9X-RAY DIFFRACTION9( CHAIN A AND RESID 46:76 )A46 - 76
10X-RAY DIFFRACTION10( CHAIN A AND RESID 77:101 )A77 - 101
11X-RAY DIFFRACTION11( CHAIN A AND RESID 102:154 )A102 - 154
12X-RAY DIFFRACTION12( CHAIN A AND RESID 155:181 )A155 - 181
13X-RAY DIFFRACTION13( CHAIN B AND RESID -5:17 )B-5 - 17
14X-RAY DIFFRACTION14( CHAIN B AND RESID 18:84 )B18 - 84
15X-RAY DIFFRACTION15( CHAIN B AND RESID 85:97 )B85 - 97
16X-RAY DIFFRACTION16( CHAIN B AND RESID 98:144 )B98 - 144
17X-RAY DIFFRACTION17( CHAIN B AND RESID 145:170 )B145 - 170
18X-RAY DIFFRACTION18( CHAIN B AND RESID 171:190 )B171 - 190

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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