[English] 日本語
Yorodumi
- PDB-2khm: Structure of the C-terminal non-repetitive domain of the spider d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2khm
TitleStructure of the C-terminal non-repetitive domain of the spider dragline silk protein ADF-3
ComponentsFibroin-3
KeywordsSTRUCTURAL PROTEIN / alpha helix / homodimer / swapped
Function / homologySpidroin domain, C-terminal domain / Spidroin, C-terminal / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Fibroin-3
Function and homology information
Biological speciesAraneus diadematus (European garden spider)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average, model 1
AuthorsHagn, F.X. / Eisoldt, L. / Hardy, J.G. / Vendrely, C. / Coles, M. / Scheibel, T. / Kessler, H.
CitationJournal: Nature / Year: 2010
Title: A conserved spider silk domain acts as a molecular switch that controls fibre assembly
Authors: Hagn, F. / Eisoldt, L. / Hardy, J.G. / Vendrely, C. / Coles, M. / Scheibel, T. / Kessler, H.
History
DepositionApr 9, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroin-3
B: Fibroin-3


Theoretical massNumber of molelcules
Total (without water)26,6592
Polymers26,6592
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)21 / 50structures with the lowest energy
RepresentativeModel #1minimized average

-
Components

#1: Protein Fibroin-3


Mass: 13329.741 Da / Num. of mol.: 2 / Fragment: UNP residues 513-636
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Araneus diadematus (European garden spider)
Gene: ADF-3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q16987
Sequence detailsTHERE ARE CONFLICTS BETWEEN SEQRES AND SEQUENCE DATABASE. THE AUTHORS BELIEVE THAT THE SEQRES IS ...THERE ARE CONFLICTS BETWEEN SEQRES AND SEQUENCE DATABASE. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the C-termial non-repetitive domain of spider dragline silk protein ADF-3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HN(CO)CA
1813D HN(CA)CO
1913D (H)CCH-TOCSY
11043D HNHA
11143D HNHB
11213D CCH-COSY
11313D C(CO)NH
11443D 1H-15N NOESY
11513D 1H-13C NOESY
11613D CNH NOESY
11743D NNH NOESY
11813D CCH NOESY
11922D 1H-1H NOESY
1203filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.3mM [U-99% 13C; U-99% 15N] NR3-1, 95% H2O/5% D2O95% H2O/5% D2O
20.6-1mM NR3-2, 95% H2O/5% D2O95% H2O/5% D2O
31mM [U-99% 13C; U-99% 15N] NR3-3, 1mM NR3-4, 95% H2O/5% D2O95% H2O/5% D2O
40.2-1mM [U-99% 15N] NR3-5, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMNR3-1[U-99% 13C; U-99% 15N]0.5-1.31
mMNR3-20.6-12
1 mMNR3-3[U-99% 13C; U-99% 15N]3
1 mMNR3-43
mMNR3-5[U-99% 15N]0.2-14
Sample conditionsIonic strength: 0.02 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502
Bruker AvanceBrukerAVANCE9003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospinprocessing
Sparky3.11Goddardpeak picking
PASTA0.1Kessler, Gemmeckerchemical shift assignment
TALOS9.4Cornilescu, Delaglio, Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorestructure solution
ProcheckNMRLaskowski, MacArthurdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 21 / Representative conformer: 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