[English] 日本語
Yorodumi
- PDB-2m0c: Solution NMR Structure of Homeobox Domain of Human ALX4, Northeas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m0c
TitleSolution NMR Structure of Homeobox Domain of Human ALX4, Northeast Structural Genomics Consortium (NESG) Target HR4490C
ComponentsHomeobox protein aristaless-like 4
KeywordsGENE REGULATION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / muscle organ development / anterior/posterior pattern specification / embryonic digit morphogenesis / roof of mouth development / hair follicle development ...HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / muscle organ development / anterior/posterior pattern specification / embryonic digit morphogenesis / roof of mouth development / hair follicle development / post-embryonic development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like ...OAR domain / OAR motif / OAR domain profile. / 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
Homeobox protein aristaless-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsXu, X. / Eletsky, A. / Pulavarti, S. / Lee, D. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Homeobox Domain of Human ALX4, Northeast Structural Genomics Consortium (NESG) Target HR4490C
Authors: Xu, X. / Eletsky, A. / Pulavarti, S. / Lee, D. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 24, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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 aristaless-like 4


Theoretical massNumber of molelcules
Total (without water)9,3571
Polymers9,3571
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 Homeobox protein aristaless-like 4 /


Mass: 9356.658 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding residues 209-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALX4, KIAA1788 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9H161

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC ali
1313D HNCO
141(4,3)D GFT CABCA(CO)NH
1512D 1H-13C HSQC aro
161(4,3)D GFT HNCABCA
1713D simultaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY ali
1111(4,3)D GFT (H)CCH-COSY ali
1121(4,3)D GFT (H)CCH-COSY aro
11312D 15N HSQC His
11422D 13C CT-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.871 mM [U-100% 13C; U-100% 15N] HR4490C, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM Tris-HCl, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [5% 13C; U-100% 15N] HR4490C, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM Tris-HCl, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.871 mMHR4490C-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTris-HCl-51
50 uMDSS-61
0.6 mMHR4490C-7[5% 13C; U-100% 15N]2
100 mMsodium chloride-82
5 mMDTT-92
0.02 %sodium azide-102
10 mMTris-HCl-112
50 uMDSS-122
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionedata analysis
AS-DP1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
PROSAGuntertdata analysis
CSIWishart and Sykesdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD
NMR constraintsNOE constraints total: 841 / NOE intraresidue total count: 188 / NOE long range total count: 205 / NOE medium range total count: 232 / NOE sequential total count: 216 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 40
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