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- PDB-5f71: Human T-cell immunoglobulin and mucin domain protein 3 (hTIM-3) -

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Basic information

Entry
Database: PDB / ID: 5f71
TitleHuman T-cell immunoglobulin and mucin domain protein 3 (hTIM-3)
ComponentsHepatitis A virus cellular receptor 2
KeywordsIMMUNE SYSTEM / Human T-cell immunoglobulin / mucin domain protein 3 / hTIM-3
Function / homology
Function and homology information


regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / positive regulation of interleukin-1 production / toll-like receptor 3 signaling pathway / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / toll-like receptor 9 signaling pathway / mediator complex / macrophage activation involved in immune response / positive regulation of macrophage activation / anchoring junction / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / immunological synapse / maternal process involved in female pregnancy / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / defense response to Gram-positive bacterium / inflammatory response / negative regulation of gene expression / innate immune response / regulation of transcription by RNA polymerase II / cell surface / metal ion binding
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
Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsGao, G.F. / Lu, G. / Wang, H. / Qi, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81590761 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08020100 China
CitationJournal: Chin.Sci.Bull. / Year: 2015
Title: Crystal structures of human TIM members: Ebolavirus entry-enhancing receptors
Authors: Wang, H. / Qi, J.X. / Liu, N.N.
History
DepositionDec 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Source and taxonomy
Revision 1.2Nov 8, 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
Item: _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: Hepatitis A virus cellular receptor 2
B: Hepatitis A virus cellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6424
Polymers24,5962
Non-polymers462
Water1,09961
1
A: Hepatitis A virus cellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3212
Polymers12,2981
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area6890 Å2
2
B: Hepatitis A virus cellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3212
Polymers12,2981
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6820 Å2
Unit cell
Length a, b, c (Å)53.997, 61.957, 67.152
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 2 / HAVcr-2 / HAVCR2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3


Mass: 12298.002 Da / Num. of mol.: 2 / Fragment: UNP residues 22-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDQ0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8M potassium sodium tartrate tetrahydrate, 0.1M sodium HEPES at pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97479 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97479 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9178 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 13.301
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.842 / Rsym value: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIX1.7.3_928refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OYP

2oyp


Resolution: 2.404→34.81 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 436 4.75 %
Rwork0.2146 --
obs0.2166 9173 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.535 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.0682 Å20 Å20 Å2
2--1.5838 Å20 Å2
3----9.652 Å2
Refinement stepCycle: LAST / Resolution: 2.404→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 2 61 1789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071774
X-RAY DIFFRACTIONf_angle_d1.2522408
X-RAY DIFFRACTIONf_dihedral_angle_d17.573642
X-RAY DIFFRACTIONf_chiral_restr0.085260
X-RAY DIFFRACTIONf_plane_restr0.008314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4041-2.75180.36111420.27752822X-RAY DIFFRACTION100
2.7518-3.46650.28131420.23422900X-RAY DIFFRACTION100
3.4665-34.81410.21361520.18493015X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.0818 Å / Origin y: 5.813 Å / Origin z: 19.1021 Å
111213212223313233
T0.1419 Å2-0.0057 Å20.0137 Å2-0.1389 Å2-0.0248 Å2--0.1422 Å2
L0.9872 °2-0.3011 °20.2494 °2-1.223 °2-0.2397 °2--0.7136 °2
S0.0269 Å °-0.0127 Å °-0.0012 Å °-0.0536 Å °0.0071 Å °-0.0732 Å °0.0407 Å °0.0059 Å °0 Å °
Refinement TLS groupSelection details: all

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