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- PDB-2or8: Tim-1 -

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Basic information

Entry
Database: PDB / ID: 2or8
TitleTim-1
ComponentsHepatitis A virus cellular receptor 1 homolog
KeywordsIMMUNE SYSTEM / Beta barrel / immunoglobulin fold / IgV domain / TIM
Function / homology
Function and homology information


positive regulation of mast cell activation / phagocytosis, engulfment / phosphatidylserine binding / brush border / response to wounding / virus receptor activity / response to lipopolysaccharide / membrane => GO:0016020 / cell surface
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Hepatitis A virus cellular receptor 1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSantiago, C. / Ballesteros, A. / Kaplan, G.G. / Casasnovas, J.M.
CitationJournal: Immunity / Year: 2007
Title: Structures of T Cell Immunoglobulin Mucin Receptors 1 and 2 Reveal Mechanisms for Regulation of Immune Responses by the TIM Receptor Family.
Authors: Santiago, C. / Ballesteros, A. / Tami, C. / Martinez-Munoz, L. / Kaplan, G.G. / Casasnovas, J.M.
History
DepositionFeb 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Hepatitis A virus cellular receptor 1 homolog
B: Hepatitis A virus cellular receptor 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0163
Polymers25,9572
Non-polymers591
Water1,874104
1
A: Hepatitis A virus cellular receptor 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0382
Polymers12,9791
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hepatitis A virus cellular receptor 1 homolog


Theoretical massNumber of molelcules
Total (without water)12,9791
Polymers12,9791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.490, 55.740, 75.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hepatitis A virus cellular receptor 1 homolog / HAVcr-1 / T cell immunoglobulin and mucin domain-containing protein 1 / TIMD-1 / T cell membrane ...HAVcr-1 / T cell immunoglobulin and mucin domain-containing protein 1 / TIMD-1 / T cell membrane protein 1 / TIM-1


Mass: 12978.605 Da / Num. of mol.: 2 / Fragment: N-terminal Cys-rich domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Knowles Solter / Gene: Havcr1, Tim1, Timd1 / Plasmid: pET-27b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5QNS5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 31.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG-2000 methylether, 5% PEG-400, 0.1M ammonium sulphate, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0552
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0552 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 6839 / Num. obs: 6839 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 13.917 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 13.1 / Net I/σ(I): 4.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2174 / Rsym value: 41.3 / % possible all: 99

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Processing

Software
NameVersionClassification
PDCdata collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Tim-2 homologous domain

Resolution: 2.5→15 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 701 -RANDOM
Rwork0.232 ---
all0.241 6851 --
obs0.241 6839 98.4 %-
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.51 Å20 Å20 Å2
2--28.11 Å20 Å2
3----13.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 4 104 1926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.74666
X-RAY DIFFRACTIONc_bond_d0.007849

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