[English] 日本語
Yorodumi
- PDB-4jkw: Structure of the extracellular domain of butyrophilin BTN3A1 in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jkw
TitleStructure of the extracellular domain of butyrophilin BTN3A1 in complex with Isopentenyl pyrophosphate (IPP)
ComponentsButyrophilin subfamily 3 member A1
KeywordsIMMUNE SYSTEM / immunoglobulin superfamily
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily ...Butyrophilin subfamily 3, PRY/SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Concanavalin A-like lectin/glucanase domain superfamily / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKumar, A. / Mori, L. / De Libero, G.
CitationJournal: Nat.Immunol. / Year: 2013
Title: Butyrophilin 3A1 binds phosphorylated antigens and stimulates human gamma delta T cells.
Authors: Vavassori, S. / Kumar, A. / Wan, G.S. / Ramanjaneyulu, G.S. / Cavallari, M. / El Daker, S. / Beddoe, T. / Theodossis, A. / Williams, N.K. / Gostick, E. / Price, D.A. / Soudamini, D.U. / ...Authors: Vavassori, S. / Kumar, A. / Wan, G.S. / Ramanjaneyulu, G.S. / Cavallari, M. / El Daker, S. / Beddoe, T. / Theodossis, A. / Williams, N.K. / Gostick, E. / Price, D.A. / Soudamini, D.U. / Voon, K.K. / Olivo, M. / Rossjohn, J. / Mori, L. / De Libero, G.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Structure summary
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Sep 25, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0192
Polymers13,7731
Non-polymers2461
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.717, 36.194, 108.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 13772.517 Da / Num. of mol.: 1 / Fragment: unp residues 28-143 / Mutation: A30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: BT3.2, BTF3, BTF4, BTF5, BTN3A1, BTN3A2, Butyrophilin subfamily 3 member A1
Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O00481
#2: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12 M ethylene glycols, 0.1 M buffer system 1, 30% PEG 550 MME and PEG 20.000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.96422 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96422 Å / Relative weight: 1
ReflectionResolution: 2.01→21.64 Å / Num. all: 7972 / Num. obs: 7571 / % possible obs: 92.76 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 19.85 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.3
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.468 / % possible all: 80

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→21.64 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.204 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.257 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26838 401 4.8 %RANDOM
Rwork0.2286 ---
obs0.23064 7571 92.76 %-
all-7972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→21.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 14 113 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021975
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9731325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.1223.72143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.669156
X-RAY DIFFRACTIONr_chiral_restr0.0680.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021738
X-RAY DIFFRACTIONr_mcbond_it0.3281.5602
X-RAY DIFFRACTIONr_mcangle_it0.6312968
X-RAY DIFFRACTIONr_scbond_it0.8413373
X-RAY DIFFRACTIONr_scangle_it1.4374.5357
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 34 -
Rwork0.194 499 -
obs--84.07 %
Refinement TLS params.Method: refined / Origin x: 9.7512 Å / Origin y: 23.9485 Å / Origin z: 70.7626 Å
111213212223313233
T0.046 Å20.0001 Å2-0.0024 Å2-0.0265 Å20.0104 Å2--0.0216 Å2
L0.9724 °2-0.0053 °2-0.2286 °2-0.412 °20.2684 °2--1.0238 °2
S0.0398 Å °-0.0032 Å °0.0179 Å °0.0241 Å °-0.011 Å °-0.0254 Å °0.0284 Å °-0.0214 Å °-0.0288 Å °

+
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