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- PDB-1dgq: NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE ... -

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Entry
Database: PDB / ID: 1dgq
TitleNMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1
ComponentsLEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1
KeywordsIMMUNE SYSTEM / ROSSMANN FOLD
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / receptor clustering / leukocyte cell-cell adhesion ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / receptor clustering / leukocyte cell-cell adhesion / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. ...Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING
AuthorsLegge, G.B. / Kriwacki, R.W. / Chung, J. / Hommel, U. / Ramage, P. / Case, D.A. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: NMR solution structure of the inserted domain of human leukocyte function associated antigen-1.
Authors: Legge, G.B. / Kriwacki, R.W. / Chung, J. / Hommel, U. / Ramage, P. / Case, D.A. / Dyson, H.J. / Wright, P.E.
History
DepositionNov 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1


Theoretical massNumber of molelcules
Total (without water)21,4261
Polymers21,4261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 100STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Representative

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Components

#1: Protein LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1


Mass: 21425.561 Da / Num. of mol.: 1 / Fragment: INSERTED DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: P20701

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
2223D 15N-SEPARATED NOESY
2323D 15N HSQC-NOESY-HSQC 140 MS MIXING TIME
NMR detailsText: NOESY MIXING TIMES OF 60 AND 100 MS FOR THE 3D 1H-15N AND 3D 1H-13C NOESY-HSQC SPECTRA. NOESY MIXING TIME OF 140 MS FOR THE 15N HSQC-NOESY-HSQC SPECTRA.

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Sample preparation

Details
Solution-IDContents
11.2 MM NMR SAMPLE OF PURIFIED AND UNIFORMLY 15N/13C ISOTOPICALLY LABELED LFA-1 I-DOMAIN
21.2 MM 15N UNIFORMLY LABELED SAMPLE WAS ALSO PREPARED IN THE FOLLOWING CONDITIONS THAT WERE LESS AFFECTED BY LINE BROADENING
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.2AMBIENT 295 K
27.3AMBIENT 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX6002
Bruker AMXBrukerAMX5003

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Processing

NMR software
NameVersionDeveloperClassification
SANE1DUGGANdata analysis
DYANA1.5GUENTERTstructure solution
Amber5.1CASEstructure solution
Amber5.1CASErefinement
RefinementMethod: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1
Details: MODEL-BASED APPROACH USED TO ASSIGN NOESY SPECTRA USING EXISTING X-RAY STRUCTURES AS A MODEL. THE STRUCTURES ARE BASED ON A TOTAL OF 5656 RESTRAINTS, 2289 ARE UNIQUE NOE-DERIVED DISTANCE ...Details: MODEL-BASED APPROACH USED TO ASSIGN NOESY SPECTRA USING EXISTING X-RAY STRUCTURES AS A MODEL. THE STRUCTURES ARE BASED ON A TOTAL OF 5656 RESTRAINTS, 2289 ARE UNIQUE NOE-DERIVED DISTANCE CONSTRAINTS, 3082 AMBIGOUS NOE-DERIVED RESTRAINTS, AND 285 DIHEDRAL ANGLE RESTRAINTS.
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 22

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