[English] 日本語
Yorodumi
- PDB-1j4v: CYANOVIRIN-N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j4v
TitleCYANOVIRIN-N
ComponentsCYANOVIRIN-N
KeywordsIMMUNE SYSTEM / CYANOVIRIN-N / HIV-INACTIVATING / DOMAIN-SWAPPED DIMER / DIPOLAR COUPLINGS / CONJOINED RIGID BODY-TORSION ANGLE DYNAMICS
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodSOLUTION NMR
AuthorsClore, G.M. / Bewley, C.A.
Citation
Journal: J.Magn.Reson. / Year: 2002
Title: Using conjoined rigid body/torsion angle simulated annealing to determine the relative orientation of covalently linked protein domains from dipolar couplings.
Authors: Clore, G.M. / Bewley, C.A.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Solution Structure of Cyanovirin-N, a Potent HIV-Inactivating Protein
Authors: Bewley, C.A. / Gustafson, K.R. / Boyd, M.R. / Covell, D.G. / Bax, A. / Clore, G.M. / Gronenborn, A.M.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of Cyanovirin-N, a Potent HIV-Inactivating Protein, Shows Unexpected Domain Swapping
Authors: Yang, F. / Bewley, C.A. / Louis, J.M. / Gustafson, K.R. / Boyd, M.R. / Gronenborn, A.M. / Clore, G.M. / Wlodawer, A.
#3: Journal: J.Am.Chem.Soc. / Year: 2000
Title: Determination of the Relative Orientation of the Two Halves of the Domain-Swapped Dimer of Cyanovirin-N in Solution Using Dipolar Couplings and Rigid Body Minimization.
Authors: Bewley, C.A. / Clore, G.M.
History
DepositionNov 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYANOVIRIN-N
B: CYANOVIRIN-N


Theoretical massNumber of molelcules
Total (without water)22,0442
Polymers22,0442
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)1 / 20RESTRAINED REGULARIZED MEAN STRUCTURE
Representative

-
Components

#1: Protein CYANOVIRIN-N / CV-N


Mass: 11022.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 6.4 / Temperature: 306 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

-
Processing

NMR softwareName: X-PLOR-NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE COORDINATES ARE NUMBERED AS FOLLOWS: SUBUNIT 1: 1-101. SUBUNIT 2: 201-301. THE DIMER IS FULLY SYMMETRIC. THE AB' HALF OF THE DIMER COMPRISES RESIDUES 1-48 and 255-301. THE A'B HALF OF ...Details: THE COORDINATES ARE NUMBERED AS FOLLOWS: SUBUNIT 1: 1-101. SUBUNIT 2: 201-301. THE DIMER IS FULLY SYMMETRIC. THE AB' HALF OF THE DIMER COMPRISES RESIDUES 1-48 and 255-301. THE A'B HALF OF THE DIMER COMPRISES RESIDUES 201-248 and 55-101. THE COORDINATES OF THE TWO HALVES OF THE DIMER ARE TAKEN FROM THE X-RAY COORDINATES (3EZM, 1.5 A RESOLUTION). THE ORIENTATION OF THE AB' HALF OF THE DIMER (RESIDUES 1-48 AND 255-301) RELATIVE TO THE A'B HALF OF THE DIMER (RESIDUES 201-248 AND 55-101) ARE DETERMINED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS ON THE BASIS OF RESIDUAL DIPOLAR COUPLINGS (68 x 2), ALLOWING ONLY THE PHI/PSI TORSION ANGLES OF RESIDUES 49-54 AND 249-254 TO ALTER THEIR CONFORMATION (SUBJECT TO NON-CRYSTALLOGRAPHIC SYMMETRY). IN ADDITION TO TERMS FOR DIPOLAR COUPLINGS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998) AND NON-CRYSTALLOGRAPHIC SYMMETRY, THE TARGET FUNCTION ALSO INCLUDES A TERM OF A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE (KUSZEWSKI AND CLORE, J. MAGN. RESON 146, 249-254 (2000)). DATA USED IN REFINEMENT: 68 x 2 1DNH DIPOLAR COUPLINGS MEASURED IN 5% C12E5 POLYETHYLENE GLYCOL/HEXANOL MIXTURE WITH A MOLAR RATIO OF SURFACTANT TO ALCOHOL OF 0.96 (PEG). AGREEMENT WITH EXPERIMENTAL DATA: DIPOLAR COUPLING R-FACTOR (CLORE AND GARRETT (1999) J. AM. CHEM. SOC. 121, 9008-9012): R-DIPOLAR (WORK/PEG) (68 x 2 COUPLINGS): 14.2% R-DIPOLAR (FREE/BICELLES) (18 x 2 COUPLINGS): 15.3% (CROSS-VALIDATED). (FOR REFERENCE, THE VALUES OF R-DIPOLAR IN PEG AND BICELLES FOR THE ORIENTATION OF THE TWO-HALVES OF THE DOMAIN-SWAPPED DIMER IN THE X-RAY COORDINATES, 3EZM, ARE 55.9% and 56.6%, RESPECTIVELY). The only protons in the coordinates are the backbone amide protons and the Ne1H proton of Trp. Note the coordinates for the two halves of the domain-swapped dimer are taken directly from the X-ray coordinates (3EZM) and their relative orientation is determined only on the basis of N-H dipolar couplings. Hence, there was no need to add the other protons to the coordinates. IN THIS ENTRY, THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES (20) AND THE MEAN COORDINATE POSITIONS. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 1-101 AND 201-301. NOTE THESE ERRORS ONLY REFLECT THE PRECISION WITH WHICH THE RELATIVE ORIENTATION OF THE TWO HALVES OF THE DOMAIN-SWAPPED DIMER HAS BEEN DETERMINED RELATIVE TO EACH OTHER. THEY DO NOT REFLECT THE ERRORS IN THE X-RAY COORDINATES OF 3EZM (WHICH ARE AROUND 0.09-0.16 A). NOTE THE OCCUPANCY FIELD HAS NO MEANING.
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 20 / Conformers submitted total number: 1

+
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://pdbjlvh1.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