[English] 日本語
Yorodumi
- PDB-4hh8: Crystal structure of bovine butyrophilin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hh8
TitleCrystal structure of bovine butyrophilin
ComponentsButyrophilin subfamily 1 member A1
KeywordsPROTEIN BINDING / Immunoglobulin Fold / milk fat globule
Function / homology
Function and homology information


regulation of immune response / regulation of cytokine production / T cell receptor signaling pathway / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. ...Butyrophilin subfamily 1/2, SPRY/PRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin 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
Butyrophilin subfamily 1 member A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEichinger, A. / Skerra, A.
CitationJournal: To be Published
Title: The extracellular region of bovine butyrophilin exhibits high structural similarity to human myelin oligodendrocyte glycoprotein
Authors: Eichinger, A. / Neumaier, I. / Skerra, A.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Butyrophilin subfamily 1 member A1


Theoretical massNumber of molelcules
Total (without water)25,2791
Polymers25,2791
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.180, 101.020, 44.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Butyrophilin subfamily 1 member A1 / BT


Mass: 25279.395 Da / Num. of mol.: 1 / Mutation: C193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BTN, BTN1A1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18892
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCES BETWEEN THE SEQUENCE OF THE SOLVED STRUCTURE AND THE DATABASE ENTRY P18892 ARISE ...THE DIFFERENCES BETWEEN THE SEQUENCE OF THE SOLVED STRUCTURE AND THE DATABASE ENTRY P18892 ARISE FROM A SPECIES-SPECIFIC VARIATION IN THE CDNA OF A THE SPECIFIC BOVINE STRAIN CLONED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.5 M potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97973,0.97985,0.96863,0.99188
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979731
20.979851
30.968631
40.991881
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 14.1 / Number: 32994 / Rsym value: 0.033 / D res high: 2.8 Å / D res low: 59.188 Å / Num. obs: 8446 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.8559.1996.510.0120.0123.4
6.268.8599.510.0250.0253.7
5.116.2699.710.0460.0463.8
4.435.1199.610.0270.0273.9
3.964.4399.510.0250.0253.9
3.613.9699.610.0340.0344
3.353.6199.510.0410.0414
3.133.3599.610.0480.0484
2.953.1399.310.060.064
2.82.9599.110.0830.0833.9
ReflectionResolution: 2.3→59.264 Å / Num. all: 15058 / Num. obs: 15058 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.059 / Net I/σ(I): 16.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.427.20.3012.51539121300.30199.1
2.42-2.577.20.213.61481220540.2199.2
2.57-2.757.20.1554.61386119190.15599.2
2.75-2.977.20.171302718100.199.5
2.97-3.257.20.0719.51188216550.07199.7
3.25-3.647.20.05511.91091415250.05599.6
3.64-4.27.10.0512.5945113370.0599.7
4.2-5.1470.05310.5816411650.05399.6
5.14-7.276.80.04213.963739350.04299.6
7.27-37.9036.10.02524.532155280.02596.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→59.26 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2848 / WRfactor Rwork: 0.2323 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8146 / SU B: 5.777 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2541 / SU Rfree: 0.2263 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.254 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 756 5 %RANDOM
Rwork0.2256 ---
obs0.2282 14285 98.92 %-
all-15094 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.5 Å2 / Biso mean: 42.1194 Å2 / Biso min: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 55 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221691
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9642290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88924.65186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24415292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5691514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211313
X-RAY DIFFRACTIONr_mcbond_it1.1531.51053
X-RAY DIFFRACTIONr_mcangle_it2.22421702
X-RAY DIFFRACTIONr_scbond_it3.0783638
X-RAY DIFFRACTIONr_scangle_it5.4054.5588
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 50 -
Rwork0.265 1044 -
all-1094 -
obs--98.83 %

+
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