[English] 日本語
Yorodumi
- PDB-5f70: Crystal structures of human TIM members -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f70
TitleCrystal structures of human TIM members
ComponentsHepatitis A virus cellular receptor 1
KeywordsIMMUNE SYSTEM / hTIM / Ebola virus / receptor
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Nov 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatitis A virus cellular receptor 1


Theoretical massNumber of molelcules
Total (without water)11,3961
Polymers11,3961
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5620 Å2
Unit cell
Length a, b, c (Å)27.787, 33.773, 86.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 11395.882 Da / Num. of mol.: 1 / Fragment: UNP residues 21-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96D42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M imidazole. 20%(v/v) Jeffamine ED-2001 (pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97972 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 7934 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 11.092
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2 / Rsym value: 0.469 / % possible all: 95.5

-
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: 2OR8

2or8


Resolution: 1.8→26.466 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 366 4.61 %
Rwork0.1972 --
obs0.2 7932 97.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.043 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.827 Å20 Å20 Å2
2--8.776 Å2-0 Å2
3---0.051 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms795 0 0 86 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007814
X-RAY DIFFRACTIONf_angle_d1.1881100
X-RAY DIFFRACTIONf_dihedral_angle_d14.538287
X-RAY DIFFRACTIONf_chiral_restr0.09124
X-RAY DIFFRACTIONf_plane_restr0.005139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7974-2.05740.28051140.22652449X-RAY DIFFRACTION98
2.0574-2.59170.30671250.18892536X-RAY DIFFRACTION99
2.5917-26.4690.23541270.19372581X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 3.0066 Å / Origin y: -0.6822 Å / Origin z: -11.0791 Å
111213212223313233
T0.174 Å20.0045 Å20.0088 Å2-0.1687 Å20.0001 Å2--0.1767 Å2
L0.5008 °2-0.0039 °20.1578 °2-0.4511 °20.0023 °2--0.6575 °2
S-0.0186 Å °0.0172 Å °-0.0442 Å °0.0638 Å °0.0036 Å °0.0304 Å °-0.0182 Å °-0.0126 Å °0 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more