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- PDB-1ah1: CTLA-4, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ah1
TitleCTLA-4, NMR, 20 STRUCTURES
ComponentsCTLA-4
KeywordsIMMUNORECEPTOR / T CELL RECEPTOR / IMMUNE RESPONSE / IMMUNOGLOBULIN
Function / homologyImmunoglobulin-like fold / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / CTLA4 inhibitory signaling / Immunoglobulin V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin-like domain superfamily / Cytotoxic T-lymphocyte antigen 4 / Immunoglobulin subtype / Immunoglobulin V-set domain / protein complex involved in cell adhesion ...Immunoglobulin-like fold / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / CTLA4 inhibitory signaling / Immunoglobulin V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin-like domain superfamily / Cytotoxic T-lymphocyte antigen 4 / Immunoglobulin subtype / Immunoglobulin V-set domain / protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / regulation of regulatory T cell differentiation / clathrin-coated endocytic vesicle / regulation of T cell proliferation / negative regulation of B cell proliferation / T cell costimulation / B cell receptor signaling pathway / adaptive immune response / immune response / external side of plasma membrane / positive regulation of apoptotic process / cellular response to DNA damage stimulus / integral component of plasma membrane / Golgi apparatus / perinuclear region of cytoplasm / plasma membrane / Cytotoxic T-lymphocyte protein 4
Function and homology information
Specimen sourceHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsMetzler, W.J. / Bajorath, J. / Fenderson, W. / Shaw, S.-Y. / Peach, R. / Constantine, K.L. / Naemura, J. / Leytze, G. / Lavoie, T.B. / Mueller, L. / Linsley, P.S.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Solution structure of human CTLA-4 and delineation of a CD80/CD86 binding site conserved in CD28.
Authors: Metzler, W.J. / Bajorath, J. / Fenderson, W. / Shaw, S.Y. / Constantine, K.L. / Naemura, J. / Leytze, G. / Peach, R.J. / Lavoie, T.B. / Mueller, L. / Linsley, P.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 11, 1997 / Release: Apr 15, 1998
RevisionDateData content typeGroupProviderType
1.0Apr 15, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTLA-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,334161
Polyers13,8651
Non-polymers31,469160
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)20 / 50LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein/peptide CTLA-4 / / CD152


Mass: 13864.697 Da / Num. of mol.: 1
Details: TETRASACCHARIDE CORE (GLCNAC, GLCNAC, FUCOSE, MANNOSE) ATTACHED AT N 78 AND N 111
Fragment: EXTRACELLULAR N-TERMINAL IMMUNOGLOBULIN V-LIKE / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Cricetulus / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16410
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 80 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-FUL / BETA-L-FUCOSE / 6-DEOXY-BETA-L-GALACTOSE


Mass: 164.156 Da / Num. of mol.: 20 / Formula: C6H12O5
#4: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 40 / Formula: C6H12O6
#5: Chemical ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 20 / Formula: C6H12O5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDType
111NOESY
121J

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Sample preparation

sample conditionspH: 7.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS 600 / Manufacturer: Varian / Model: UNITYPLUS 600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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