[English] 日本語
Yorodumi
- PDB-2kcx: Solution NMR Structure of Kazal-1 Domain of Human Follistatin-rel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kcx
TitleSolution NMR Structure of Kazal-1 Domain of Human Follistatin-related protein 3 (FSTL-3). Northeast Structural Genomics Target HR6186A.
ComponentsFollistatin-related protein 3
Keywordsstructural genomics / unknown function / Kazal-1 / Follistatin / Chromosomal rearrangement / Glycoprotein / Nucleus / Proto-oncogene / Secreted / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / NUCLEOTIDE-BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / Antagonism of Activin by Follistatin / regulation of BMP signaling pathway / positive regulation of cell-cell adhesion / activin binding / negative regulation of activin receptor signaling pathway / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / hematopoietic progenitor cell differentiation ...negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway / Antagonism of Activin by Follistatin / regulation of BMP signaling pathway / positive regulation of cell-cell adhesion / activin binding / negative regulation of activin receptor signaling pathway / negative regulation of osteoclast differentiation / fibronectin binding / negative regulation of BMP signaling pathway / hematopoietic progenitor cell differentiation / ossification / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell differentiation / endoplasmic reticulum lumen / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Follistatin, N-terminal / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 ...Follistatin, N-terminal / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Follistatin-related protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Chiang, Y. / Anderson, S. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Kazal-1 Domain of Human Follistatin-related protein 3 (FSTL-3). Northeast Structural Genomics Target HR6186A.
Authors: Rossi, P. / Chiang, Y. / Anderson, S. / Montelione, G.T.
History
DepositionDec 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Follistatin-related protein 3


Theoretical massNumber of molelcules
Total (without water)7,9811
Polymers7,9811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Follistatin-related protein 3 / Follistatin-like 3 / Follistatin-related gene protein


Mass: 7981.164 Da / Num. of mol.: 1 / Fragment: Kazal-1 domain, residues 97-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FSTL3, FLRG, UNQ674/PRO1308 / Production host: Escherichia coli (E. coli) / References: UniProt: O95633

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HN(CA)CB
1713D HNCO
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D CCH-TOCSY
11213D HNCA
11322D 1H-15N HET NOE
11422D N15 T1
11522D N15 T2 CPMG
11622D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] FSTL-3-1, 20 mM MES-2, 200 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM [U-100% 15N] FSTL-3-4, 20 mM MES-5, 200 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMFSTL-3-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
0.2 mMFSTL-3-4[U-100% 15N]2
20 mMMES-52
200 mMsodium chloride-62
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
PSVS1.3Bhattacharya and Montelionestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky2.113Goddarddata analysis
TopSpin2.1Bruker Biospincollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichvisualization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorefinement
MolProbityRichardsonrefinement
PdbStatTejero, Montelionedata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) (MS) = 516.1/136.2, TAUC = 3.94(NS). CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE ...Details: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) (MS) = 516.1/136.2, TAUC = 3.94(NS). CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 98.10%, SIDECHAIN 88.50%, AROMATIC (SC) 75.00%. STRUCTURE BASED ON 912 NOE, 65 DIHE. MAX NOE VIOLATION: 0.19 A (1MODEL); MAX DIHE VIOLATION: 5.4 DEG. 6 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 4-9, 13-27, 33-34, 37-58, 61-69, 72-73 FOR [S(PHI)+S(PSI)] > 1.8. SECONDARY STRUCTURE - ALPHA HELICES: 50-60, BETA STRANDS: 13-18, 21-26, 46-47, 39-41, 66-69. RMSD 1.3 BACKBONE, 1.8 ALL HEAVY ATOMS. RAMA. DISTRIBUTION: 92.1/7.8/0.1/0.0. PROCHECK (PSI-PHI): -0.34/-1.02 (RAW/Z), PROCHECK (ALL): -0.33/-1.95 (RAW/Z), MOLPROBITY CLASH: 19.69/-1.85 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.99, PRECISION: 0.85, F-MEASURE: 0.91, DP-SCORE: 0.82.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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