[English] 日本語
Yorodumi
- PDB-2kl7: Solution NMR Structure of the EGF-like 1 Domain of Human Fibulin-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kl7
TitleSolution NMR Structure of the EGF-like 1 Domain of Human Fibulin-4. Northeast Structural Genomics Target HR6275
ComponentsFibulin-4
KeywordsSIGNALING PROTEIN / STRUCTURAL PROTEIN / secreted / Calcium / Disease mutation / Disulfide bond / EGF-like domain / Glycoprotein / Polymorphism / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / METAL BINDING PROTEIN
Function / homology
Function and homology information


elastic fiber assembly / Molecules associated with elastic fibres / extracellular matrix structural constituent / basement membrane / extracellular vesicle / collagen-containing extracellular matrix / calcium ion binding / extracellular exosome / extracellular region
Similarity search - Function
EGF-containing fibulin-like extracellular matrix protein 2 / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain ...EGF-containing fibulin-like extracellular matrix protein 2 / Complement Clr-like EGF domain / Complement Clr-like EGF-like / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
EGF-containing fibulin-like extracellular matrix protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular 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 the EGF-like 1 Domain of Human Fibulin-4. Northeast Structural Genomics Target HR6275
Authors: Rossi, P. / Chiang, Y. / Anderson, S. / Montelione, G.T.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Fibulin-4


Theoretical massNumber of molelcules
Total (without water)7,5761
Polymers7,5761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Fibulin-4 / EGF-containing fibulin-like extracellular matrix protein 2 / FIBL-4 / Protein UPH1


Mass: 7576.424 Da / Num. of mol.: 1 / Fragment: EGF-like 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EFEMP2, FBLN4, UNQ200/PRO226 / Production host: Escherichia coli (E. coli) / References: UniProt: O95967

-
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 HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D HN(CA)CO
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11213D CCH-TOCSY
11312D 1H-15N HMQC
11412D 1H-15N het NOE
11511D 15N T1 series
11611D 15N T2 series
11722D 1H-15N HSQC
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) T1=664.9 MS T2=128.48 MS TAUC=4.8 NS. CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. STRUCTURE DETERMINED ...Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2(CPMG) T1=664.9 MS T2=128.48 MS TAUC=4.8 NS. CONSISTENT WITH MOLECULAR WEIGHT OF MONOMERIC UNIT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. ASSIGNMENT STATS (ALL RESIDUES INCLUDED): BACKBONE 91.89%, SIDECHAIN 83.74%, AROMATIC (SC) 100%. UNAMBIGUOUS SIDECHAIN NH2 100%.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 15N] protein, 150 mM sodium chloride, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMprotein-1[U-100% 13C; U-100% 15N]1
150 mMsodium chloride-21
20 mMMES-31
50 uMDSS-41
0.3 mMprotein-5[U-100% 15N]2
150 mMsodium chloride-62
20 mMMES-72
50 uMDSS-82
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1Bruker Biospincollection
PSVS1.3Bhattacharya and Montelionevalidation
Sparky2.113Goddarddata analysis
PINEBahrami, Markley, Assadi, and Eghbalniadata analysis
MOLMOLKoradi, Billeter and Wuthrichvisualization
PyMOLDeLano Scientificvisualization
PdbStat5.1Tejero, Montelionepdb processing
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL ...Details: NOESY ASSIGNMENTS BY CYANA-3.0. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA-3.0. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). STRUCTURE BASED ON 776 NOE, 106 DIHE. MAX NOE VIOLATION: 0.23 A (1MODEL); MAX DIHE VIOLATION: 7.1 DEG. 1 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES: 11-34,53-66 (FINDCORE). SECONDARY STRUCTURE - BETA STRANDS: 17-21, 25-29, 61-63. RMSD(ANG): BACKBONE 1.0, ALL HEAVY ATOMS 1.3. RAMA. DISTRIBUTION: 94.1/5.9/0.0/0.0. PROCHECK (PSI-PHI): -0.38/-1.18 (RAW/Z), PROCHECK (ALL): -0.22/-1.30 (RAW/Z), MOLPROBITY CLASH: 16.14/-1.24 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.880, PRECISION: 0.916, F-MEASURE: 0.898, DP-SCORE: 0.651.
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://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