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- PDB-5f7h: Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) c... -

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Basic information

Entry
Database: PDB / ID: 5f7h
TitleHuman T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) complex with phosphoserine
ComponentsT-cell immunoglobulin and mucin domain-containing protein 4
KeywordsIMMUNE SYSTEM / complex / hTIM-4 / phosphoserine
Function / homology
Function and homology information


cytoskeletal rearrangement involved in phagocytosis, engulfment / apoptotic cell clearance / phosphatidylserine binding / extracellular region / plasma membrane
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHOSERINE / T-cell immunoglobulin and mucin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: T-cell immunoglobulin and mucin domain-containing protein 4
A: T-cell immunoglobulin and mucin domain-containing protein 4
C: T-cell immunoglobulin and mucin domain-containing protein 4
D: T-cell immunoglobulin and mucin domain-containing protein 4
E: T-cell immunoglobulin and mucin domain-containing protein 4
F: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35618
Polymers76,0056
Non-polymers1,35112
Water2,090116
1
B: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: T-cell immunoglobulin and mucin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8933
Polymers12,6671
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.444, 65.034, 68.851
Angle α, β, γ (deg.)90.00, 108.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
T-cell immunoglobulin and mucin domain-containing protein 4 / TIMD-4 / T-cell immunoglobulin mucin receptor 4 / TIM-4 / T-cell membrane protein 4


Mass: 12667.476 Da / Num. of mol.: 6 / Fragment: UNP residues 24-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMD4, TIM4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96H15
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: hTIM-4 crystals were soaked in reservoir solution with the addition of 20 mM O-Phospho-L-serine (sigma-aldrich) and 5 mM CaCl2 for 20 h.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30954 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 12.143
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.333 / Rsym value: 0.81 / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIX1.8.2_1309refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BI9

3bi9


Resolution: 2.5→48.216 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1427 4.61 %
Rwork0.2097 --
obs0.2128 30928 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 72 116 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085462
X-RAY DIFFRACTIONf_angle_d1.287384
X-RAY DIFFRACTIONf_dihedral_angle_d15.0752012
X-RAY DIFFRACTIONf_chiral_restr0.075828
X-RAY DIFFRACTIONf_plane_restr0.005936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.492-2.5810.41641420.3452688X-RAY DIFFRACTION91
2.581-2.68440.41571720.30162857X-RAY DIFFRACTION98
2.6844-2.80650.33831510.26952911X-RAY DIFFRACTION99
2.8065-2.95450.3481380.24122998X-RAY DIFFRACTION100
2.9545-3.13960.30821320.23862996X-RAY DIFFRACTION100
3.1396-3.38190.2731620.20212948X-RAY DIFFRACTION100
3.3819-3.72210.23861380.18722972X-RAY DIFFRACTION100
3.7221-4.26040.27781280.18643032X-RAY DIFFRACTION100
4.2604-5.36660.21481130.17073034X-RAY DIFFRACTION100
5.3666-48.2250.24261510.2043065X-RAY DIFFRACTION99

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