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- PDB-1jl4: CRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN FRAGMENT... -

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Basic information

Entry
Database: PDB / ID: 1jl4
TitleCRYSTAL STRUCTURE OF THE HUMAN CD4 N-TERMINAL TWO DOMAIN FRAGMENT COMPLEXED TO A CLASS II MHC MOLECULE
Components
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K ALPHA CHAIN
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K BETA CHAIN
  • OVOTRANSFERRIN
  • T-CELL SURFACE GLYCOPROTEIN CD4
KeywordsIMMUNE SYSTEM / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


extracellular sequestering of iron ion / organomineral extracellular matrix / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / Downstream TCR signaling ...extracellular sequestering of iron ion / organomineral extracellular matrix / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / Downstream TCR signaling / maintenance of protein location in cell / T cell selection / antigen processing and presentation of peptide antigen / MHC class II protein binding / MHC class II antigen presentation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / antimicrobial humoral response / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / positive regulation of T cell differentiation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / intracellular sequestering of iron ion / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / antigen processing and presentation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / negative regulation of T cell proliferation / protein tyrosine kinase binding / positive regulation of interleukin-2 production / T cell activation / multivesicular body / ferric iron binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / acute-phase response / clathrin-coated endocytic vesicle membrane / recycling endosome / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / cell surface receptor protein tyrosine kinase signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / virus receptor activity / signaling receptor activity / Clathrin-mediated endocytosis / MHC class II protein complex binding / late endosome membrane / antibacterial humoral response / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / response to lipopolysaccharide / 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 surface receptor signaling pathway / early endosome / cell adhesion / immune response / response to xenobiotic stimulus / positive regulation of protein phosphorylation / iron ion binding / membrane raft / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / cell surface / signal transduction / protein homodimerization activity / extracellular space
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 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. ...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 / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / H-2 class II histocompatibility antigen, A-K alpha chain / Ovotransferrin / H-2 class II histocompatibility antigen, A-K beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsWang, J.-H. / Meijers, R. / Reinherz, E.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the human CD4 N-terminal two-domain fragment complexed to a class II MHC molecule.
Authors: Wang, J.H. / Meijers, R. / Xiong, Y. / Liu, J.H. / Sakihama, T. / Zhang, R. / Joachimiak, A. / Reinherz, E.L.
History
DepositionJul 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K ALPHA CHAIN
B: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K BETA CHAIN
C: OVOTRANSFERRIN
D: T-CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)63,7444
Polymers63,7444
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.195, 145.195, 103.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K ALPHA CHAIN


Mass: 20429.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01910
#2: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-K BETA CHAIN


Mass: 21887.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06343
#3: Protein/peptide OVOTRANSFERRIN / / CONALBUMIN


Mass: 1700.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P02789
#4: Protein T-CELL SURFACE GLYCOPROTEIN CD4 / T-CELL SURFACE ANTIGEN T4/LEU-3


Mass: 19725.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01730

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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: 4.29 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% PEG 4,000/0.2M Li2SO4/0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
217 %PEG40001reservoir
30.2 M1reservoirLi2SO4
40.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 12, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4.3→30 Å / Num. all: 7428 / Num. obs: 7428 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.152 / Net I/σ(I): 12
Reflection shellResolution: 4.3→4.5 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / % possible all: 56
Reflection
*PLUS
% possible obs: 83 % / Redundancy: 9.6 %
Reflection shell
*PLUS
% possible obs: 56 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
EPMRphasing
FFFEARmodel building
REFMACrefinement
FFFEARphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAK and 3CD4

1iak

3cd4


Resolution: 4.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS MODEL IS BASED ON HIGH RESOLUTION STRUCTURES OF THE INDIVIDUAL COMPONENTS AND ONLY RIGID BODY REFINEMENT OF THE INDIVIDUAL DOMAINS WAS APPLIED. THE RIGID BODIES CONSISTED OF RESIDUE ...Details: THIS MODEL IS BASED ON HIGH RESOLUTION STRUCTURES OF THE INDIVIDUAL COMPONENTS AND ONLY RIGID BODY REFINEMENT OF THE INDIVIDUAL DOMAINS WAS APPLIED. THE RIGID BODIES CONSISTED OF RESIDUE RANGES A 5 TO A 85, A 86 TO A 181, B 5 TO B 85, B 86 TO B 190, C 131 TO C 146, D 1 TO D 97 AND D 98 TO D 178
RfactorNum. reflection% reflectionSelection details
Rfree0.453 649 -RANDOM
Rwork0.42 ---
all0.428 6432 --
obs0.428 6432 81 %-
Refinement stepCycle: LAST / Resolution: 4.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 0 0 4474
LS refinement shellResolution: 4.3→4.5 Å
RfactorNum. reflection% reflection
Rfree0.48 94 -
Rwork0.48 --
obs-941 56 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 4.3 Å / σ(F): 0 / Rfactor Rwork: 0.42
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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