[English] 日本語
Yorodumi
- PDB-1mpv: Structure of bhpBR3, the BAFF-binding loop of BR3 embedded in a b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mpv
TitleStructure of bhpBR3, the BAFF-binding loop of BR3 embedded in a beta-hairpin peptide
ComponentsBLyS Receptor 3
KeywordsPROTEIN BINDING / beta-hairpin
Function / homology
Function and homology information


B cell costimulation / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / positive regulation of B cell proliferation / T cell costimulation / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
MethodSOLUTION NMR / hybrid distance geometry, simulated annealing, restrained molecular dynamics.
AuthorsKayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. ...Kayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. / Starovasnik, M.A. / Dixit, V.M.
CitationJournal: Immunity / Year: 2002
Title: BAFF/BLyS receptor 3 binds the B cell survival factor BAFF ligand through a discrete surface loop and promotes processing of NF-kappaB2.
Authors: Kayagaki, N. / Yan, M. / Seshasayee, D. / Wang, H. / Lee, W. / French, D.M. / Grewal, I.S. / Cochran, A.G. / Gordon, N.C. / Yin, J. / Starovasnik, M.A. / Dixit, V.M.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THIS IS PART OF AN OPTIMIZED BETA-HAIRPIN SCAFFOLD, (SEE RUSSELL, BLANDL, SKELTON, & ...SEQUENCE THIS IS PART OF AN OPTIMIZED BETA-HAIRPIN SCAFFOLD, (SEE RUSSELL, BLANDL, SKELTON, & COCHRAN, "STABILITY OF CYCLIC BETA-HAIRPINS: ASYMMETRIC CONTRIBUTIONS FROM SIDE CHAINS OF A HYDROGEN-BONDED CROSS-STRAND RESIDUE PAIR", J. AMER. CHEM. SOC., IN PRESS.)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLyS Receptor 3


Theoretical massNumber of molelcules
Total (without water)1,5941
Polymers1,5941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide BLyS Receptor 3 / Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF ...Tumor necrosis factor receptor superfamily member 13C / B cell-activating factor receptor / BAFF receptor / BAFF-R / BLys receptor 3


Mass: 1593.918 Da / Num. of mol.: 1 / Fragment: BR3 loop (residues 26-31) / Source method: obtained synthetically
Details: The Peptide was synthesized chemically with acetylated N-terminus and amidated C-terminus
References: UniProt: Q96RJ3
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
152COSY-35

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.9 mM bhpBR3 peptide92% H2O, 8% D2O, 0.1 mM DSS, pH 4.5
22.9 mM bhpBR3 peptide100% D2O, 0.1 mM DSS, pH 4.5
Sample conditionsIonic strength: no added salt / pH: 4.5 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.37.4.2Brukercollection
Felix98Accelrysdata analysis
DGII98Accelrysstructure solution
Discover98Accelrysrefinement
RefinementMethod: hybrid distance geometry, simulated annealing, restrained molecular dynamics.
Software ordinal: 1
Details: Complete 1H resonance assignments were obtained using standard 2D homonuclear NMR methods. Distance restraints were derived from analysis of a 2D NOESY spectrum (250ms mixing time); HN-Ha ...Details: Complete 1H resonance assignments were obtained using standard 2D homonuclear NMR methods. Distance restraints were derived from analysis of a 2D NOESY spectrum (250ms mixing time); HN-Ha coupling constants were obtained from analysis of a DQF-COSY spectrum acquired in water; and HaHb values were obtained from analysis of a COSY-35 spectrum acquired in D2O. Structures were calculated from a total of 119 NOE-derived (including 46 long-range) distance restraints and 16 dihedral angle restraints. Structures satisfy the experimental data very well with no distance or dihedral angle violations greater than 0.1 angstrom or 1 degree, respectively.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

+
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