[English] 日本語
Yorodumi
- PDB-4f9l: Crystal Structure of the Human BTN3A1 Ectodomain in Complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f9l
TitleCrystal Structure of the Human BTN3A1 Ectodomain in Complex with the 20.1 Single Chain Antibody
Components
  • 20.1 anti-BTN3A1 antibody fragment
  • Butyrophilin subfamily 3 member A1
KeywordsIMMUNE SYSTEM / B7 superfamily / Butyrophilin / CD277
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 / signaling receptor binding / external side of plasma membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1404 Å
AuthorsPalakodeti, A. / Sandstrom, A. / Sundaresan, L. / Harly, C. / Nedellec, S. / Olive, D. / Scotet, E. / Bonneville, M. / Adams, E.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The molecular basis for modulation of human V(gamma)9V(delta)2 T cell responses by CD277/Butyrophilin-3 (BTN3A)-specific antibodies
Authors: Palakodeti, A. / Sandstrom, A. / Sundaresan, L. / Harly, C. / Nedellec, S. / Olive, D. / Scotet, E. / Bonneville, M. / Adams, E.J.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
D: 20.1 anti-BTN3A1 antibody fragment
C: 20.1 anti-BTN3A1 antibody fragment
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3506
Polymers101,9074
Non-polymers4422
Water00
1
A: Butyrophilin subfamily 3 member A1
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7244
Polymers47,2812
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-6 kcal/mol
Surface area20810 Å2
MethodPISA
2
D: 20.1 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)27,3131
Polymers27,3131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 20.1 anti-BTN3A1 antibody fragment


Theoretical massNumber of molelcules
Total (without water)27,3131
Polymers27,3131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.136, 165.136, 53.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEGLYGLYchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA2 - 1275 - 130
121ILEILEGLYGLYchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA133 - 183136 - 186
131GLUGLUSERSERchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA187 - 195190 - 198
141GLYGLYILEILEchain 'A' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )AA199 - 208202 - 211
211PHEPHEGLYGLYchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD2 - 1275 - 130
221ILEILEGLYGLYchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD133 - 183136 - 186
231GLUGLUSERSERchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD187 - 195190 - 198
241GLYGLYILEILEchain 'B' and (resseq 2:127 or resseq 133:183 or resseq 187:195 or resseq 199:208 )BD199 - 208202 - 211
112ASPASPASPASPchain 'D' and (resseq 1:105 )DB1 - 1051 - 105
212ASPASPASPASPchain 'C' and (resseq 1:105 )CC1 - 1051 - 105

NCS ensembles :
ID
1
2

-
Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 23640.660 Da / Num. of mol.: 2 / Fragment: Ectodomain (UNP Residues 30-246)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF5, BTN3A1 / Plasmid: pAcGP67A / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: O00481
#2: Antibody 20.1 anti-BTN3A1 antibody fragment


Mass: 27312.916 Da / Num. of mol.: 2
Fragment: domains of the heavy and light chains of the 20.1 antibody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG / Plasmid: pAK300 / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.15M Potassium Fluoride, 14% PEG 3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. all: 25881 / Num. obs: 25881 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 75.17 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.14-3.2199.1
3.2-3.26199.9
3.26-3.331100
3.33-3.391100
3.39-3.471100
3.47-3.551100
3.55-3.641100
3.64-3.731100
3.73-3.841100
3.84-3.971100
3.97-4.111100
4.11-4.271100
4.27-4.471100
4.47-4.71100
4.7-51100
5-5.381100
5.38-5.931100
5.93-6.781100
6.78-8.54199.9
8.54-50199.3

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F80, 1IGT

4f80

1igt


Resolution: 3.1404→45.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7634 / SU ML: 0.74 / σ(F): 1.33 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 1326 5.13 %
Rwork0.2538 --
obs0.2564 25831 99.72 %
all-25881 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.127 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 233.2 Å2 / Biso mean: 85.6031 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.7611 Å2-0 Å20 Å2
2---4.7611 Å2-0 Å2
3---9.5221 Å2
Refinement stepCycle: LAST / Resolution: 3.1404→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 28 0 6598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076811
X-RAY DIFFRACTIONf_angle_d1.2199269
X-RAY DIFFRACTIONf_chiral_restr0.0751049
X-RAY DIFFRACTIONf_plane_restr0.0051193
X-RAY DIFFRACTIONf_dihedral_angle_d19.7832367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1424X-RAY DIFFRACTIONPOSITIONAL0.052
12B1424X-RAY DIFFRACTIONPOSITIONAL0.052
21D802X-RAY DIFFRACTIONPOSITIONAL0.081
22C802X-RAY DIFFRACTIONPOSITIONAL0.081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1404-3.26610.38331370.3432672280999
3.2661-3.41470.37631330.314727112844100
3.4147-3.59470.31921410.289627222863100
3.5947-3.81980.34941370.270426752812100
3.8198-4.11460.30061550.265927252880100
4.1146-4.52830.27291410.223327152856100
4.5283-5.18280.25861520.212327162868100
5.1828-6.52670.29761610.253327382899100
6.5267-45.80530.29941690.24122831300099

+
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