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- PDB-3s4s: Crystal structure of CD4 mutant bound to HLA-DR1 -

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Basic information

Entry
Database: PDB / ID: 3s4s
TitleCrystal structure of CD4 mutant bound to HLA-DR1
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Hemagglutinin peptide
  • T-cell surface glycoprotein CD4
KeywordsIMMUNE SYSTEM / protein-protein complex
Function / homology
Function and homology information


regulation of interleukin-4 production / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-10 production / response to methamphetamine hydrochloride / maintenance of protein location in cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / cellular response to ionomycin ...regulation of interleukin-4 production / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of interleukin-10 production / response to methamphetamine hydrochloride / maintenance of protein location in cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / cellular response to ionomycin / autolysosome membrane / regulation of T-helper cell differentiation / T cell selection / 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 / MHC class II protein binding / 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 / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / Nef Mediated CD4 Down-regulation / Alpha-defensins / CD4 receptor binding / response to vitamin D / intermediate filament / regulation of T cell activation / extracellular matrix structural constituent / T-helper 1 type immune response / Other interleukin signaling / T cell receptor complex / transport vesicle membrane / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of calcium ion transport into cytosol / polysaccharide binding / positive regulation of protein kinase activity / negative regulation of type II interferon production / regulation of calcium ion transport / humoral immune response / Generation of second messenger molecules / macrophage differentiation / immunological synapse / T cell differentiation / immunoglobulin binding / Co-inhibition by PD-1 / epidermis development / Binding and entry of HIV virion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / coreceptor activity / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / MHC class II antigen presentation / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Vpu mediated degradation of CD4 / 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 / calcium-mediated signaling / 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 / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / transmembrane signaling receptor activity / positive regulation of protein phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / response to estradiol / signaling receptor activity / T cell receptor signaling pathway / Clathrin-mediated endocytosis / virus receptor activity / early endosome membrane / response to ethanol / defense response to Gram-negative bacterium / clathrin-dependent endocytosis of virus by host cell / adaptive immune response
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / 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 ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / 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 / Immunoglobulin / Immunoglobulin domain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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
T-cell surface glycoprotein CD4 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Affinity maturation of human CD4 by yeast surface display and crystal structure of a CD4-HLA-DR1 complex.
Authors: Wang, X.X. / Li, Y. / Yin, Y. / Mo, M. / Wang, Q. / Gao, W. / Wang, L. / Mariuzza, R.A.
History
DepositionMay 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, DRB1-1 beta chain
C: Hemagglutinin peptide
G: T-cell surface glycoprotein CD4
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: Hemagglutinin peptide
H: T-cell surface glycoprotein CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,01411
Polymers132,7388
Non-polymers2763
Water1,22568
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: Hemagglutinin peptide
G: T-cell surface glycoprotein CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4615
Polymers66,3694
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: Hemagglutinin peptide
H: T-cell surface glycoprotein CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5536
Polymers66,3694
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.260, 137.290, 88.290
Angle α, β, γ (deg.)90.000, 106.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE

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


Mass: 21145.887 Da / Num. of mol.: 2 / Fragment: UNP residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22456.133 Da / Num. of mol.: 2 / Fragment: UNP residues 30-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide / Protein , 2 types, 4 molecules CFGH

#3: Protein/peptide Hemagglutinin peptide


Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: UNP residues 306-318
Source method: isolated from a genetically manipulated source
Details: strain - A/Swine/Netherlands/L2/93(H3N2) / Source: (synth.) Influenza A virus / References: UniProt: Q9YS52, UniProt: P03437*PLUS
#4: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 21260.059 Da / Num. of mol.: 2 / Fragment: UNP residues 26-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Plasmid: pAcGP67-B / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01730

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Non-polymers , 2 types, 71 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, (NH4)SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.502 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 60345 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Χ2: 1.023 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.495.50.59959920.802199.6
2.49-2.595.70.47959960.836199.6
2.59-2.75.70.39660440.874199.8
2.7-2.855.70.27659870.91199.8
2.85-3.025.70.20560010.977199.8
3.02-3.265.80.15560411.035199.7
3.26-3.585.80.11160171.187199.8
3.58-4.160.0960491.241199.9
4.1-5.175.90.06860851.2021100
5.17-506.30.06361331.1161100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2856 3011 5 %
Rwork0.2508 --
obs-59805 99.8 %
Solvent computationBsol: 46.2536 Å2
Displacement parametersBiso max: 88.81 Å2 / Biso mean: 45.14 Å2 / Biso min: 10.74 Å2
Baniso -1Baniso -2Baniso -3
1-17.862 Å20 Å2-8.209 Å2
2---16.465 Å20 Å2
3----1.397 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8838 0 18 68 8924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.381
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3gol.param

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