[English] 日本語
Yorodumi
- PDB-2jrf: Solution NMR structure of Tubulin polymerization-promoting protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jrf
TitleSolution NMR structure of Tubulin polymerization-promoting protein family member 3 from Homo sapiens. Northeast Structural Genomics target HR387.
ComponentsTubulin polymerization-promoting protein family member 3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


microtubule bundle formation / positive regulation of protein polymerization / microtubule polymerization / decidualization / embryo implantation / tubulin binding / microtubule / cytoplasm
Similarity search - Function
Tubulin polymerisation-promoting protein family member 3 / P25-alpha / p25-alpha / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tubulin polymerization-promoting protein family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Rossi, P. / Shastry, R. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Rajan, P.K. / Acton, T.B. ...Aramini, J.M. / Rossi, P. / Shastry, R. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Rajan, P.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Tubulin polymerization-promoting protein family member 3 from Homo sapiens.
Authors: Aramini, J.M. / Rossi, P. / Shastry, R. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Rajan, P.K. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Remark 999 SEQUENCE AUTHORS STATE THAT THE SEQUENCE CONFLICT AT POSITION 7 IS A CLONING ARTIFACT DUE TO ... SEQUENCE AUTHORS STATE THAT THE SEQUENCE CONFLICT AT POSITION 7 IS A CLONING ARTIFACT DUE TO SEQUENCE ANNOTATION ERROR.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin polymerization-promoting protein family member 3


Theoretical massNumber of molelcules
Total (without water)20,0741
Polymers20,0741
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Tubulin polymerization-promoting protein family member 3


Mass: 20073.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein is a monomer by gel filtration and static light scattering.
Gene: TPPP3 / Plasmid: HR387-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MK / References: UniProt: Q9BW30

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 1H-13C NOESY aromatic
1613D HNCO
1713D HN(CA)CO
1813D HN(COCA)CB
1913D HN(CA)CB
11013D C(CO)NH-TOCSY
11113D CCH-TOCSY
11213D CCH-TOCSY aromatic
11313D (H)CCH-COSY
11413D HNHA
11513D (H)CCH-TOCSY
11622D 1H-13C HSQC high res.
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.1%, SIDE CHAIN, 88.3%, AROMATICS, 91.8%, STEREOSPECIFIC METHYL, 65.0%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 178, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 9-19,23-24,28-45,53-62,69-86,92-103: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 95.0%, ADDITIONALLY ALLOWED, 5.0%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.26/1.34, ALL, 0.18/1.06. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 12.78/-0.67. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-178): RECALL, 0.972, PRECISION, 0.878, F-MEASURE, 0.922, DP-SCORE, 0.726. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI) + S(PSI) < 1.8): 1-8,20-22,25-27,46-52,63-68,87-91,104-178

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.04 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-5% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.04 mMhr387[U-100% 13C; U-100% 15N]1
20 mMammonium acetate1
100 mMsodium chloride1
10 mMDTT1
5 mMcalcium chloride1
0.02 %sodium azide1
0.7 mMhr387[U-5% 13C; U-100% 15N]2
20 mMammonium acetate2
10 mMDTT2
5 mMcalcium chloride2
0.02 %sodium azide2
Sample conditionsIonic strength: 100 mM / pH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
PdbStat5Tejero and Montelionepdb analysis
TALOSCornilescu, Delaglio and Baxdihedral angle constraints
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1554 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 120 DIHEDRAL ANGLE CONSTRAINTS, AND 74 HYDROGEN BOND CONSTRAINTS (11.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1554 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 120 DIHEDRAL ANGLE CONSTRAINTS, AND 74 HYDROGEN BOND CONSTRAINTS (11.4 CONSTRAINTS PER RESIDUE, 2.6 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 178 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS).
NMR constraintsNOE constraints total: 1554 / NOE intraresidue total count: 317 / NOE long range total count: 392 / NOE medium range total count: 405 / NOE sequential total count: 440
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.4 ° / Maximum upper distance constraint violation: 0.24 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

+
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