[English] 日本語
Yorodumi
- PDB-2lp0: The solution structure of homeodomain-protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lp0
TitleThe solution structure of homeodomain-protein complex
Components
  • Geminin
  • Homeobox protein Hox-C9
KeywordsTRANSCRIPTION/CELL CYCLE / homeodomain / TRANSCRIPTION-CELL CYCLE complex
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / embryonic skeletal system morphogenesis / proximal/distal pattern formation / aggresome / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / anterior/posterior pattern specification / negative regulation of DNA replication ...DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / embryonic skeletal system morphogenesis / proximal/distal pattern formation / aggresome / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / anterior/posterior pattern specification / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / regulation of mitotic cell cycle / transcription repressor complex / Assembly of the pre-replicative complex / animal organ morphogenesis / histone deacetylase binding / transcription corepressor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / Hox9 activation region / Geminin/Multicilin / Geminin / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. ...Hox9, N-terminal activation domain / Homeobox protein HXA9/HXB9/HXC9 / Hox9 activation region / Geminin/Multicilin / Geminin / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Geminin / Homeobox protein Hox-C9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, C. / Zhou, B. / Xu, Z. / Zhu, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for homeodomain recognition by the cell-cycle regulator Geminin
Authors: Zhou, B. / Liu, C. / Xu, Z. / Zhu, G.
History
DepositionJan 29, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox protein Hox-C9
B: Geminin


Theoretical massNumber of molelcules
Total (without water)10,0692
Polymers10,0692
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)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Homeobox protein Hox-C9 / Homeobox protein Hox-3B


Mass: 7739.212 Da / Num. of mol.: 1 / Fragment: UNP residues 192-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXC9 / Production host: Escherichia coli (E. coli) / References: UniProt: P31274
#2: Protein/peptide Geminin


Mass: 2330.237 Da / Num. of mol.: 1 / Fragment: UNP residues 171-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMNN / Production host: Escherichia coli (E. coli) / References: UniProt: O75496

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-13C HSQC
1422D 1H-13C HSQC
1513D HNCO
1613D HN(CA)CB
1713D CBCA(CO)NH
1833D (H)CCH-TOCSY
1913D 1H-15N NOESY
11033D 1H-13C NOESY aliphatic
11123D HNCO
11223D CBCA(CO)NH
11323D HN(CA)CB
11423D 1H-15N NOESY
11543D 1H-13C NOESY aliphatic
11643D (H)CCH-TOCSY
11733D 13C-FILTERED 13C-EDITED NOESY
11843D 13C-FILTERED 13C-EDITED NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] Hox-C9-1, 1.0 mM Geminin-2, 25 mM potassium phosphate-3, 100 mM sodium chloride-4, 5 mM DTT-5, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM Hox-C9-6, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-7, 25 mM potassium phosphate-8, 100 mM sodium chloride-9, 5 mM DTT-10, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] Hox-C9-11, 1.0 mM Geminin-12, 25 mM potassium phosphate-13, 100 mM sodium chloride-14, 5 mM DTT-15, 100% D2O100% D2O
41.0 mM Hox-C9-16, 0.8 mM [U-100% 13C; U-100% 15N] Geminin-17, 25 mM potassium phosphate-18, 100 mM sodium chloride-19, 5 mM DTT-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHox-C9-1[U-100% 13C; U-100% 15N]1
1.0 mMGeminin-21
25 mMpotassium phosphate-31
100 mMsodium chloride-41
5 mMDTT-51
1.0 mMHox-C9-62
0.8 mMGeminin-7[U-100% 13C; U-100% 15N]2
25 mMpotassium phosphate-82
100 mMsodium chloride-92
5 mMDTT-102
0.8 mMHox-C9-11[U-100% 13C; U-100% 15N]3
1.0 mMGeminin-123
25 mMpotassium phosphate-133
100 mMsodium chloride-143
5 mMDTT-153
1.0 mMHox-C9-164
0.8 mMGeminin-17[U-100% 13C; U-100% 15N]4
25 mMpotassium phosphate-184
100 mMsodium chloride-194
5 mMDTT-204
Sample conditionsIonic strength: 0.125 / pH: 6.5 / Pressure: ambient / Temperature: 296 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
ProcheckNMRLaskowski and MacArthurgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
HADDOCKAlexandre Bonvinrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10 / 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