[English] 日本語
Yorodumi
- PDB-6akp: Crystal Structural of FOXC2 DNA binding domain bound to PC promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6akp
TitleCrystal Structural of FOXC2 DNA binding domain bound to PC promoter
Components
  • DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
  • Forkhead box protein C2
KeywordsDNA BINDING PROTEIN/DNA / FOXC / DNA binding domain / DNA recognition / Crystal Structural / Lymphoedema distichiasis syndrome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / glomerular endothelium development / Formation of intermediate mesoderm / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / glomerular mesangial cell development / Formation of the ureteric bud / podocyte differentiation / lymphangiogenesis / neural crest cell development / regulation of organ growth / metanephros development / embryonic heart tube development / camera-type eye development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / negative regulation of cold-induced thermogenesis / ventricular cardiac muscle tissue morphogenesis / cardiac muscle cell proliferation / artery morphogenesis / ureteric bud development / DNA-binding transcription activator activity / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / somitogenesis / Notch signaling pathway / positive regulation of endothelial cell migration / blood vessel diameter maintenance / ossification / response to hormone / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...: / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 Å
AuthorsChen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 China
National Natural Science Foundation of China81570537 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for DNA recognition by FOXC2.
Authors: Chen, X. / Wei, H. / Li, J. / Liang, X. / Dai, S. / Jiang, L. / Guo, M. / Qu, L. / Chen, Z. / Chen, L. / Chen, Y.
History
DepositionSep 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
B: DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')
C: Forkhead box protein C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1474
Polymers22,1233
Non-polymers241
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-24 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.837, 80.214, 101.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')


Mass: 4896.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Forkhead box protein C2 / Forkhead-related protein FKHL14 / Mesenchyme fork head protein 1 / MFH-1 protein / Transcription factor FKH-14


Mass: 12330.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXC2, FKHL14, MFH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99958
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50mM NaOAc pH4.7, 14%PEG4K, 200mM NaCl, 10mM MgCl2, 0.5mM TCEP

-
Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.323→37.29 Å / Num. obs: 15111 / % possible obs: 98 % / Redundancy: 13.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1289 / Net I/σ(I): 13.97
Reflection shellResolution: 2.323→2.407 Å / Rmerge(I) obs: 0.9166 / Num. unique obs: 1366 / CC1/2: 0.913

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X07

5x07


Resolution: 2.323→37.283 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.12
RfactorNum. reflection% reflection
Rfree0.247 1505 10.03 %
Rwork0.2174 --
obs0.2204 15012 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.323→37.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 650 1 16 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041548
X-RAY DIFFRACTIONf_angle_d0.652224
X-RAY DIFFRACTIONf_dihedral_angle_d22.608805
X-RAY DIFFRACTIONf_chiral_restr0.035233
X-RAY DIFFRACTIONf_plane_restr0.003176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3235-2.39850.41531200.36261095X-RAY DIFFRACTION91
2.3985-2.48420.33331350.33111207X-RAY DIFFRACTION98
2.4842-2.58360.35951360.31311226X-RAY DIFFRACTION99
2.5836-2.70120.32871350.30841207X-RAY DIFFRACTION100
2.7012-2.84350.30471380.29741235X-RAY DIFFRACTION100
2.8435-3.02160.34361370.30271237X-RAY DIFFRACTION100
3.0216-3.25480.29091350.27891209X-RAY DIFFRACTION98
3.2548-3.58210.3151390.23741223X-RAY DIFFRACTION98
3.5821-4.09990.24841390.20671259X-RAY DIFFRACTION99
4.0999-5.16320.17971420.17271278X-RAY DIFFRACTION100
5.1632-37.28810.19461490.15821331X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5063-0.1883-0.77922.7209-0.75992.34310.6968-0.0847-1.4723-0.15410.95080.03372.5221-2.1791-1.67651.7296-0.1176-0.09251.31140.15261.1552-32.141372.628210.7602
25.31770.96271.47772.29830.07122.11840.6611-0.420.74271.4590.6405-2.23360.76670.6058-0.97530.844-0.0658-0.01770.91240.08821.0006-26.357182.840423.8216
31.9748-0.26110.35064.9175-1.9264.34180.273-0.7748-0.41960.65850.74520.0614-0.4074-1.3696-0.40751.1002-0.002-0.00840.9476-0.00510.7449-27.985178.669443.627
44.00083.9283-0.10097.87290.23992.12670.46630.9310.107-0.8732-0.1376-0.4007-3.1174-1.2746-0.10321.50710.1504-0.1541.08570.03510.9234-24.481285.940344.1005
53.0646-1.5837-0.75711.9446-1.50172.13590.44390.4123-0.51870.268-0.021-0.54480.702-0.8879-0.1770.994-0.004-0.08970.85320.05040.7387-28.835978.348719.7119
63.5744-0.21671.44772.429-0.11532.90950.21240.05290.7436-0.2958-0.2222-0.11620.0032-0.25210.00190.45540.01970.0230.3730.06820.4955-39.612994.53892.3863
75.7678-2.4925-0.26557.427-3.6195.6157-0.2534-1.55940.01660.89220.4562-0.288-0.96670.2366-0.49460.5717-0.10920.00230.6824-0.01990.6416-28.6235101.356911.1076
89.0726-1.62992.68463.7052-1.18936.5191-0.2935-0.81531.25880.7116-0.2805-0.0005-0.4723-0.7750.26180.62130.0273-0.01040.6158-0.00140.5335-39.391794.706912.1747
91.3523-1.20651.27325.66310.19462.56980.2515-1.1813-0.92610.8895-0.62440.51620.8377-0.82880.06320.6327-0.09990.03070.8240.14040.7432-48.001890.25049.2385
105.17250.260.31094.4171-0.54832.3230.0106-0.6563-0.53340.17330.06170.00650.9640.2714-0.09820.77470.0482-0.0150.48090.05280.6706-36.03284.45377.9734
118.29492.45685.59327.19511.76863.7860.53560.8449-1.1928-0.73720.0104-0.42120.50120.8073-0.07780.59110.05890.0510.8194-0.04180.7208-24.87590.91993.8281
122.2018-1.2346-1.7180.67110.96851.31580.8052-0.68820.95342.21870.71970.8332-0.11880.7608-1.40151.077-0.0395-0.07591.37120.17591.1601-23.541994.506617.8955
132.84970.00410.14492.6753-0.02931.2356-0.0236-0.1071-0.1514-0.3479-0.1939-0.32660.378-0.16610.04350.5323-0.020.05640.72140.06690.6538-30.249698.1432-0.9593
142.8002-1.3087-1.79796.86671.70213.2417-0.65561.16920.2372-0.64190.9864-1.30941.0993-0.4758-0.08891.0915-0.21340.17431.3139-0.20530.9789-29.928494.0615-10.2621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 18 )
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 24 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 13 )
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 24 )
6X-RAY DIFFRACTION6chain 'C' and (resid 70 through 87 )
7X-RAY DIFFRACTION7chain 'C' and (resid 88 through 94 )
8X-RAY DIFFRACTION8chain 'C' and (resid 95 through 105 )
9X-RAY DIFFRACTION9chain 'C' and (resid 106 through 112 )
10X-RAY DIFFRACTION10chain 'C' and (resid 113 through 126 )
11X-RAY DIFFRACTION11chain 'C' and (resid 127 through 133 )
12X-RAY DIFFRACTION12chain 'C' and (resid 134 through 144 )
13X-RAY DIFFRACTION13chain 'C' and (resid 145 through 162 )
14X-RAY DIFFRACTION14chain 'C' and (resid 163 through 168 )

+
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