[English] 日本語
Yorodumi
- PDB-8ft9: Crystal structure of a new antigen receptor variable domain from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ft9
TitleCrystal structure of a new antigen receptor variable domain from nurse sharks
ComponentsVNAR B6
KeywordsANTITOXIN / Variable New Antigen Receptor (VNAR)
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesGinglymostoma cirratum (nurse shark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsYerabham, A.S.K. / Hsieh, C.M. / Fu, Y. / Bou-Nader, C. / Cachau, R. / Zhang, J. / Ho, M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Z01 BC010891 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC010891 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIC BC 011891 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIADK075136 United States
CitationJournal: To Be Published
Title: Crystal structure of a new antigen receptor variable domain from nurse sharks
Authors: Yerabham, A.S.K. / Fu, Y. / Hsieh, C.M. / Bou-Nader, C. / Cachau, R. / Zhang, J. / Ho, M.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VNAR B6
B: VNAR B6
C: VNAR B6
D: VNAR B6
E: VNAR B6
F: VNAR B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,29518
Polymers86,1586
Non-polymers1,13712
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.824, 89.891, 186.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
VNAR B6


Mass: 14359.642 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 percent PEG 8000 and 0.2 M potassium nitrate. HT crystallization screen Wizard PEG-Ion 48 Salt with PEG 8K and 10K from Molecular Dimensions

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→43.7 Å / Num. obs: 26818 / % possible obs: 96.68 % / Redundancy: 5.98 % / CC1/2: 0.965 / CC star: 0.9911 / Rmerge(I) obs: 0.365 / Rrim(I) all: 0.402 / Net I/σ(I): 4.23
Reflection shellResolution: 2.74→2.838 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.022 / Num. unique obs: 2472 / CC1/2: 0.792 / CC star: 0.9402 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→43.7 Å / SU ML: 0.4083 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.9759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2775 1342 5.01 %
Rwork0.2396 25470 -
obs0.2414 26812 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.28 Å2
Refinement stepCycle: LAST / Resolution: 2.74→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 61 163 5200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245119
X-RAY DIFFRACTIONf_angle_d0.46376933
X-RAY DIFFRACTIONf_chiral_restr0.0411763
X-RAY DIFFRACTIONf_plane_restr0.0039872
X-RAY DIFFRACTIONf_dihedral_angle_d4.5213735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.840.36291300.32592472X-RAY DIFFRACTION96.05
2.84-2.950.3611340.31052546X-RAY DIFFRACTION98.67
2.95-3.080.36531360.31132563X-RAY DIFFRACTION98
3.09-3.250.36461300.28042486X-RAY DIFFRACTION95.72
3.25-3.450.30861360.25312577X-RAY DIFFRACTION98.8
3.45-3.720.25111340.23872550X-RAY DIFFRACTION97.81
3.72-4.090.24611340.20462559X-RAY DIFFRACTION96.84
4.09-4.680.18691320.16732496X-RAY DIFFRACTION94.46
4.68-5.90.21371360.19482591X-RAY DIFFRACTION97.22
5.9-43.70.30541400.25362630X-RAY DIFFRACTION93.23

+
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://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