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- PDB-1gya: N-GLYCAN AND POLYPEPTIDE NMR SOLUTION STRUCTURES OF THE ADHESION ... -

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Basic information

Entry
Database: PDB / ID: 1gya
TitleN-GLYCAN AND POLYPEPTIDE NMR SOLUTION STRUCTURES OF THE ADHESION DOMAIN OF HUMAN CD2
ComponentsHUMAN CD2
KeywordsADHESION GLYCOPROTEIN / CELL SURFACE ADHESION RECEPTOR / IMMUNOGLOBULIN SUPERFAMILY V-SET DOMAIN / T LYMPHOCYTE ADHESION GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / cell-cell adhesion ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / cell-cell adhesion / receptor tyrosine kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / signaling receptor activity / cell surface receptor signaling pathway / immune response / signaling receptor binding / external side of plasma membrane / apoptotic process / cell surface / Golgi apparatus / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsWyss, D.F. / Choi, J.S. / Wagner, G.
Citation
Journal: Science / Year: 1995
Title: Conformation and function of the N-linked glycan in the adhesion domain of human CD2.
Authors: Wyss, D.F. / Choi, J.S. / Li, J. / Knoppers, M.H. / Willis, K.J. / Arulanandam, A.R. / Smolyar, A. / Reinherz, E.L. / Wagner, G.
#1: Journal: Biochemistry / Year: 1995
Title: Composition and Sequence Specific Resonance Assignments of the Heterogeneous N-Linked Glycan in the 13.6 KDa Adhesion Domain of Human Cd2 as Determined by NMR on the Intact Glycoprotein
Authors: Wyss, D.F. / Choi, J.S. / Wagner, G.
History
DepositionMay 26, 1995Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 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
A: HUMAN CD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0132
Polymers12,4531
Non-polymers1,5591
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 120PROSTAT/STRUCT_CHECK
Representative

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Components

#1: Protein HUMAN CD2 / HSCD2=105=


Mass: 12453.215 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN
Source method: isolated from a genetically manipulated source
Details: GLYCOSYLATED / Source: (gene. exp.) Homo sapiens (human)
Description: THE ADHESION DOMAIN OF HUMAN CD2 (HSCD2=105=) WAS OBTAINED BY CLOSTRIPAIN DIGESTION OF THE TWO-DOMAIN HUMAN CD2 (HSCD2=182=)
Gene: SCD2=182= / Organ: OVARY / Plasmid: PM1 / Gene (production host): SCD2=182= / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06729
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 4.5 / Temperature: 286 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameDeveloperClassification
DGIIHAVELrefinement
DGIIstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: PROSTAT/STRUCT_CHECK / Conformers calculated total number: 120 / Conformers submitted total number: 18

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