[English] 日本語
Yorodumi
- PDB-2mdg: Solution NMR Structure of Zinc finger protein 423 from Homo sapie... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mdg
TitleSolution NMR Structure of Zinc finger protein 423 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7298F
ComponentsZinc finger protein 423
KeywordsDNA BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target HR7298F / PSI-Biology / Protein Structure Initiative / C2H2
Function / homology
Function and homology information


protein localization to cilium / positive regulation of BMP signaling pathway / negative regulation of cold-induced thermogenesis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Notch signaling pathway / nervous system development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...protein localization to cilium / positive regulation of BMP signaling pathway / negative regulation of cold-induced thermogenesis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Notch signaling pathway / nervous system development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
C2H2-type zinc finger / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein 423
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailsfewest violations, model6
AuthorsPederson, K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Zinc finger protein 423 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7298F
Authors: Pederson, K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Prestegard, J.H.
History
DepositionSep 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger protein 423
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4683
Polymers6,3371
Non-polymers1312
Water00
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 least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Zinc finger protein 423 / Olf1/EBF-associated zinc finger protein / hOAZ / Smad- and Olf-interacting zinc finger protein


Mass: 6337.325 Da / Num. of mol.: 1 / Fragment: UNP residues 928-981
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0760, NPHP14, OAZ, ZNF423 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q2M1K9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: The NESG target Hr7298F contains two C2H2 zinc finger motifs between residues 928 and 981 of the Homo sapiens Zinc finger protein 423. Residual dipolar couplings suggest that the two zinc ...Details: The NESG target Hr7298F contains two C2H2 zinc finger motifs between residues 928 and 981 of the Homo sapiens Zinc finger protein 423. Residual dipolar couplings suggest that the two zinc finger motifs are connected by flexible loops and not restricted with respect to one another. Therefore the positions of domains with respect to one another in the structures reported are not significant.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1833D 1H-15N NOESY
1913D 1H-13C NOESY aliphatic
11032D 1H-13C CT HSQC
11112D 1H-15N J-modulation HSQC
11222D 1H-15N J-modulation HSQC
11312D 1H-15N CO filtered TROSY
11442D 1H-15N CO-filtered TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.17 mM [U-100% 13C; U-100% 15N] HR7298F.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % [U-100% 2H] D2O, 50 uM DSS, 50 uM ZnSO4, 90% H2O/10% D2O90% H2O/10% D2O
20.51 mM [U-5% 13C; U-100% 15N] HR7298F.0059, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % [U-100% 2H] D2O, 50 uM DSS, 4.2 % C12E5 PEG/Hexanol, 50 uM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
30.51 mM [U-5% 13C; U-100% 15N] HR7298F.009, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % [U-100% 2H] D2O, 50 uM DSS, 50 uM ZnSO4, 95% H2O/5% D2O95% H2O/5% D2O
40.17 mM [U-100% 13C; U-100% 15N] HR7298F.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % [U-100% 2H] D2O, 50 uM DSS, 50 uM ZnSO4, 4.2 % C12E5 PEG?Hexanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.17 mMHR7298F.005-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-8[U-100% 2H]1
0.050 mMDSS-91
0.050 mMZnSO4-101
0.51 mMHR7298F.0059-11[U-5% 13C; U-100% 15N]2
0.02 %NaN3-122
10 mMDTT-132
5 mMCaCL2-142
100 mMNaCL-152
1 %Proteinase Inhibitors-162
20 mMMES pH 6.5-172
10 %D2O-18[U-100% 2H]2
0.050 mMDSS-192
4.2 %C12E5 PEG/Hexanol-202
0.050 mMZnSO4-212
0.51 mMHR7298F.009-22[U-5% 13C; U-100% 15N]3
0.02 %NaN3-233
10 mMDTT-243
5 mMCaCL2-253
100 mMNaCL-263
1 %Proteinase Inhibitors-273
20 mMMES pH 6.5-283
10 %D2O-29[U-100% 2H]3
0.050 mMDSS-303
0.050 mMZnSO4-313
0.17 mMHR7298F.005-32[U-100% 13C; U-100% 15N]4
0.02 %NaN3-334
10 mMDTT-344
5 mMCaCL2-354
100 mMNaCL-364
1 %Proteinase Inhibitors-374
20 mMMES pH 6.5-384
10 %D2O-39[U-100% 2H]4
0.050 mMDSS-404
0.050 mMZnSO4-414
4.2 %C12E5 PEG?Hexanol-424
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian AvanceVarianAVANCE9002
Varian AvanceVarianAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
Sparky3.113Goddardchemical shift assignment
PALESPALES (Zweckstetter, Bax)structure validation
PSVS1.5Bhattacharya, Montelionestructure validation
CNSrefinement
NMR constraintsNOE constraints total: 330 / NOE intraresidue total count: 146 / NOE long range total count: 50 / NOE medium range total count: 41 / NOE sequential total count: 93 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 38
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
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