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- PDB-4x5x: HLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W) -

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Basic information

Entry
Database: PDB / ID: 4x5x
TitleHLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W)
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / MHC II / SELF ANTIGEN / INVARIANT CHAIN / CLIP
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 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 / Generation of second messenger molecules / macrophage differentiation / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / negative regulation of T cell proliferation / T cell receptor binding / MHC class II antigen presentation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / Interferon gamma signaling / positive regulation of T cell activation / endocytic vesicle membrane / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / adaptive immune response / lysosome / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / cell surface / signal transduction / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.199 Å
AuthorsGuenther, S. / Freund, C.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationFR-1325/11-1 Germany
German Research FoundationSFB 765 Germany
German Research Foundation854 Germany
German Research Foundation958 Germany
CitationJournal: Nat Commun / Year: 2016
Title: MHC class II complexes sample intermediate states along the peptide exchange pathway.
Authors: Wieczorek, M. / Sticht, J. / Stolzenberg, S. / Gunther, S. / Wehmeyer, C. / El Habre, Z. / Alvaro-Benito, M. / Noe, F. / Freund, C.
History
DepositionDec 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 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, DRB1-1 beta chain
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1-1 beta chain


Theoretical massNumber of molelcules
Total (without water)96,2304
Polymers96,2304
Non-polymers00
Water00
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain


Theoretical massNumber of molelcules
Total (without water)48,1152
Polymers48,1152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-32 kcal/mol
Surface area18470 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1-1 beta chain


Theoretical massNumber of molelcules
Total (without water)48,1152
Polymers48,1152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-34 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.821, 86.467, 94.110
Angle α, β, γ (deg.)90.000, 103.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHEchain AAA2 - 1803 - 181
21GLUGLUPHEPHEchain CCC4 - 1805 - 181
12METMETTRPTRPchain BBB-30 - 1881 - 219
22METMETTRPTRPchain DDD-30 - 1881 - 219

NCS ensembles :
ID
1
2
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22353.223 Da / Num. of mol.: 2 / Fragment: extracellular, UNP residues 26-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR1


Mass: 25761.893 Da / Num. of mol.: 2 / Fragment: extracellular, UNP residues 30-227 / Mutation: N82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET24D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04229, UniProt: P01911*PLUS
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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / Details: mirrors
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.199→34.25 Å / Num. obs: 14844 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.17 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.192 / Net I/σ(I): 5.5 / Num. measured all: 45860
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
3.2-3.423.10.4732.5826326670.81799.4
9.05-34.2530.0712.219476600.99594.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å34.19 Å
Translation3.2 Å34.19 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
Aimless0.2.17data scaling
PHASERphasing
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dlh

1dlh


Resolution: 3.199→34.247 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 765 5.16 %
Rwork0.2201 14052 -
obs0.2223 14817 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.16 Å2 / Biso mean: 44.0737 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 3.199→34.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 0 0 6130
Num. residues----752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026304
X-RAY DIFFRACTIONf_angle_d0.6938563
X-RAY DIFFRACTIONf_chiral_restr0.027920
X-RAY DIFFRACTIONf_plane_restr0.0041113
X-RAY DIFFRACTIONf_dihedral_angle_d13.4532297
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1670X-RAY DIFFRACTION7.218TORSIONAL
12C1670X-RAY DIFFRACTION7.218TORSIONAL
21B1801X-RAY DIFFRACTION7.218TORSIONAL
22D1801X-RAY DIFFRACTION7.218TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1988-3.44550.30621630.27362794295799
3.4455-3.79190.30661310.23922809294099
3.7919-4.33960.25721690.21112806297599
4.3396-5.46390.22091720.18792784295699
5.4639-34.24920.25391300.21192859298998

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