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- PDB-5dzo: Crystal structure of human T-cell immunoglobulin and mucin domain... -

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Basic information

Entry
Database: PDB / ID: 5dzo
TitleCrystal structure of human T-cell immunoglobulin and mucin domain protein 1
ComponentsHepatitis A virus cellular receptor 1
KeywordsIMMUNE SYSTEM / receptor / Ig V domain
Function / homology
Function and homology information


positive regulation of mast cell activation / motile cilium / phagocytosis, engulfment / phosphatidylserine binding / virus receptor activity / Attachment and Entry / cell surface / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Hepatitis A virus cellular receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 Å
AuthorsYuan, S. / Rao, Z. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology 973 Project2014CB542800 China
CitationJournal: Protein Cell / Year: 2015
Title: TIM-1 acts a dual-attachment receptor for Ebolavirus by interacting directly with viral GP and the PS on the viral envelope.
Authors: Yuan, S. / Cao, L. / Ling, H. / Dang, M. / Sun, Y. / Zhang, X. / Chen, Y. / Zhang, L. / Su, D. / Wang, X. / Rao, Z.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9944
Polymers11,8471
Non-polymers1473
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.739, 50.739, 84.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 11846.519 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR1, KIM1, TIM1, TIMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96D42
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5 M sodium nitrate, 0.1 M sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 27042 / % possible obs: 97.4 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.017 / Net I/av σ(I): 34.178 / Net I/σ(I): 10.4 / Num. measured all: 328083
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.358.50.17321960.88981.8
1.35-1.4110.15126130.87895.9
1.4-1.46130.13126891.03999.2
1.46-1.5412.60.11127131.07699.2
1.54-1.6412.60.09627300.92199.2
1.64-1.76130.08427201.04899.4
1.76-1.9412.30.07327571.06999.6
1.94-2.2212.90.06427951.08299.9
2.22-2.812.60.05728231.01799.9
2.8-50120.06830061.06199.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.301→33.004 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1761 1282 4.75 %
Rwork0.1565 --
obs0.1574 26993 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.301→33.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 9 156 990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013859
X-RAY DIFFRACTIONf_angle_d1.4111164
X-RAY DIFFRACTIONf_dihedral_angle_d12.359306
X-RAY DIFFRACTIONf_chiral_restr0.068131
X-RAY DIFFRACTIONf_plane_restr0.008149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3011-1.35320.16861130.152350X-RAY DIFFRACTION83
1.3532-1.41480.17741310.15192802X-RAY DIFFRACTION97
1.4148-1.48940.17981560.15112851X-RAY DIFFRACTION99
1.4894-1.58270.16421280.14252892X-RAY DIFFRACTION99
1.5827-1.70490.14781580.14842860X-RAY DIFFRACTION99
1.7049-1.87650.17581610.15492881X-RAY DIFFRACTION100
1.8765-2.1480.17371210.15512961X-RAY DIFFRACTION100
2.148-2.7060.18771710.16622961X-RAY DIFFRACTION100
2.706-33.01470.17841430.15833153X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8591-0.0778-0.51510.773-0.24551.82030.0366-0.04980.0090.0255-0.0012-0.0235-0.07790.048-0.03540.0957-0.0107-0.00270.0881-0.00830.099618.08790.469710.9214
23.2987-1.4673-0.27090.8319-0.03880.1627-0.01840.0382-0.2413-0.0712-0.04510.12320.27730.0576-0.01070.16370.01440.00540.0928-0.00420.120721.0495-11.70933.7992
32.06730.9603-0.52111.9982-0.81410.6115-0.10330.11830.0171-0.27320.0365-0.02970.24150.03550.0020.1271-0.00370.01350.0943-0.00630.07518.5827-1.5061-0.0393
41.7302-0.54391.7141.00170.72024.8903-0.19280.4660.32740.01330.00490.0575-0.54790.14990.16860.1524-0.00820.00640.1090.03350.168320.08255.1207-2.65
57.1132.70441.90932.29240.52442.8779-0.0291-0.02930.2496-0.0323-0.02270.1039-0.2115-0.10510.00330.10620.02550.00550.07390.00580.091212.36624.66813.5189
66.75013.7394-2.7528.88481.0524.12050.153-0.12680.1962-0.00340.0133-0.4202-0.53690.3095-0.010.1531-0.0298-0.00120.0924-0.00420.120824.74328.6239.1006
74.29120.1104-0.61890.8814-0.28271.30320.0101-0.01970.0288-0.01350.02070.0683-0.0038-0.1425-0.02080.0817-0.0096-0.00190.0853-0.00560.060211.3477-2.0538.8835
83.4603-1.991-0.2281.1570.35914.5568-0.02540.04820.48380.0120.1237-0.49650.17960.2718-0.10770.12560.0165-0.01440.1728-0.00340.15333.727-7.08563.7242
92.00750.1831-2.53651.5652-0.33623.2599-0.0197-0.222-0.19270.05970.02990.12880.0846-0.0314-0.07670.1106-00.00130.10980.00140.085212.4783-4.672914.7132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 47 )
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 55 )
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 72 )
7X-RAY DIFFRACTION7chain 'A' and (resid 73 through 90 )
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 98 )
9X-RAY DIFFRACTION9chain 'A' and (resid 99 through 110 )

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