[English] 日本語
Yorodumi
- PDB-7vox: The crystal structure of human forkhead box protein A in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vox
TitleThe crystal structure of human forkhead box protein A in complex with DNA 2
Components
  • DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
  • Hepatocyte nuclear factor 3-alpha
KeywordsTRANSCRIPTION/DNA / DNA-protein complex / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / lung epithelial cell differentiation ...alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / mesenchymal-epithelial cell signaling involved in prostate gland development / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / epithelial cell maturation involved in prostate gland development / neuron fate specification / lung epithelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / dorsal/ventral neural tube patterning / prostate gland epithelium morphogenesis / dopaminergic neuron differentiation / Formation of axial mesoderm / positive regulation of smoothened signaling pathway / hormone metabolic process / negative regulation of epithelial to mesenchymal transition / smoothened signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / epithelial tube branching involved in lung morphogenesis / microvillus / anatomical structure morphogenesis / Notch signaling pathway / positive regulation of mitotic cell cycle / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / fibrillar center / sequence-specific double-stranded DNA binding / glucose homeostasis / response to estradiol / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of apoptotic process / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. ...Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChoi, Y. / Yoon, H.J. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2B2008142 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations.
Authors: Choi, Y. / Luo, Y. / Lee, S. / Jin, H. / Yoon, H.J. / Hahn, Y. / Bae, J. / Lee, H.H.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
G: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
A: Hepatocyte nuclear factor 3-alpha
B: Hepatocyte nuclear factor 3-alpha
C: Hepatocyte nuclear factor 3-alpha
H: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32810
Polymers67,2798
Non-polymers492
Water8,035446
1
D: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
A: Hepatocyte nuclear factor 3-alpha
C: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6645
Polymers33,6404
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-45 kcal/mol
Surface area14270 Å2
MethodPISA
2
F: DNA (5'-D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3')
G: DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')
B: Hepatocyte nuclear factor 3-alpha
H: Hepatocyte nuclear factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6645
Polymers33,6404
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-41 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.547, 144.291, 75.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-448-

HOH

21C-331-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 169 through 188 or resid 191...
21(chain B and (resid 169 through 188 or resid 191...
31(chain C and (resid 169 through 188 or resid 191...
41(chain H and (resid 169 through 188 or resid 191...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSER(chain A and (resid 169 through 188 or resid 191...AE169 - 1887 - 26
12LEULEUGLNGLN(chain A and (resid 169 through 188 or resid 191...AE191 - 21229 - 50
13TRPTRPPROPRO(chain A and (resid 169 through 188 or resid 191...AE214 - 23552 - 73
14LYSLYSGLYGLY(chain A and (resid 169 through 188 or resid 191...AE237 - 23975 - 77
15GLYGLYASPASP(chain A and (resid 169 through 188 or resid 191...AE241 - 24979 - 87
21ALAALASERSER(chain B and (resid 169 through 188 or resid 191...BF169 - 1887 - 26
22LEULEUGLNGLN(chain B and (resid 169 through 188 or resid 191...BF191 - 21229 - 50
23TRPTRPPROPRO(chain B and (resid 169 through 188 or resid 191...BF214 - 23552 - 73
24LYSLYSGLYGLY(chain B and (resid 169 through 188 or resid 191...BF237 - 23975 - 77
25GLYGLYASPASP(chain B and (resid 169 through 188 or resid 191...BF241 - 24979 - 87
31ALAALASERSER(chain C and (resid 169 through 188 or resid 191...CG169 - 1887 - 26
32LEULEUGLNGLN(chain C and (resid 169 through 188 or resid 191...CG191 - 21229 - 50
33TRPTRPPROPRO(chain C and (resid 169 through 188 or resid 191...CG214 - 23552 - 73
34LYSLYSGLYGLY(chain C and (resid 169 through 188 or resid 191...CG237 - 23975 - 77
35GLYGLYASPASP(chain C and (resid 169 through 188 or resid 191...CG241 - 24979 - 87
41ALAALASERSER(chain H and (resid 169 through 188 or resid 191...HH169 - 1887 - 26
42LEULEUGLNGLN(chain H and (resid 169 through 188 or resid 191...HH191 - 21229 - 50
43TRPTRPPROPRO(chain H and (resid 169 through 188 or resid 191...HH214 - 23552 - 73
44LYSLYSGLYGLY(chain H and (resid 169 through 188 or resid 191...HH237 - 23975 - 77
45GLYGLYASPASP(chain H and (resid 169 through 188 or resid 191...HH241 - 24979 - 87

-
Components

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


Mass: 4895.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3')


Mass: 4895.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Hepatocyte nuclear factor 3-alpha / HNF-3-alpha / HNF-3A / Forkhead box protein A1 / Transcription factor 3A / TCF-3A


Mass: 11924.612 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA1, HNF3A, TCF3A / Production host: Escherichia coli (E. coli) / References: UniProt: P55317
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 6% Tacsimate pH 6.0, and 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 44236 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.26 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.037 / Rrim(I) all: 0.113 / Χ2: 1.001 / Net I/σ(I): 6.3 / Num. measured all: 406203
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.149.10.61621790.9220.2140.6530.599100
2.14-2.189.30.54321970.9270.1870.5750.582100
2.18-2.229.40.45821690.9470.1570.4840.588100
2.22-2.268.90.68621880.9330.2430.7291.622100
2.26-2.319.40.3821910.9560.130.4020.622100
2.31-2.379.40.3521910.9510.120.370.61100
2.37-2.429.30.27321820.9760.0940.2890.635100
2.42-2.499.20.2422030.9790.0840.2550.625100
2.49-2.568.90.20121890.9810.0710.2130.642100
2.56-2.658.20.17721720.9820.0650.1890.641100
2.65-2.748.60.21422080.9840.0760.2280.96100
2.74-2.859.20.13722160.9820.0480.1450.78100
2.85-2.989.80.12321960.9920.0410.130.823100
2.98-3.149.70.10122210.9940.0350.1070.979100
3.14-3.339.80.08622060.9950.0310.0921.16100
3.33-3.599.50.08822230.9950.0310.0931.506100
3.59-3.959.30.0922340.9970.0310.0951.824100
3.95-4.5290.06822410.9970.0240.0721.53100
4.52-5.78.10.0722580.9950.0260.0751.59100
5.7-509.50.06223720.9970.0210.0661.63999.7

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CBY

7cby


Resolution: 2.1→43.984 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1914 4.65 %
Rwork0.1858 39234 -
obs0.1871 41148 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.17 Å2 / Biso mean: 34.462 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 2.1→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 1312 2 446 4564
Biso mean--9.4 37.86 -
Num. residues----402
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A864X-RAY DIFFRACTION8.801TORSIONAL
12B864X-RAY DIFFRACTION8.801TORSIONAL
13C864X-RAY DIFFRACTION8.801TORSIONAL
14H864X-RAY DIFFRACTION8.801TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1003-2.15280.2894890.2324208770
2.1528-2.2110.25611100.2163223875
2.211-2.27610.24061370.2139239480
2.2761-2.34950.26561320.2186256587
2.3495-2.43350.24091330.209274292
2.4335-2.53090.27011090.2164295398
2.5309-2.64610.23341270.2152297899
2.6461-2.78560.27441460.21673016100
2.7856-2.96010.2541320.21753007100
2.9601-3.18850.23151370.1963008100
3.1885-3.50930.20681760.16672986100
3.5093-4.01680.1811420.15743051100
4.0168-5.05960.15951880.1483026100
5.0596-43.9840.18151560.17563183100
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)
10.10330.010.01720.01420.03550.07120.0464-0.09370.2165-0.0684-0.0088-0.0188-0.033-0.1094-0.00320.1521-0.19220.08520.2101-0.04390.2879-28.526212.214619.6267
20.02-0.0184-0.00860.02220.00410.01420.0238-0.08330.1820.0503-0.03230.0233-0.0148-0.0248-0.07980.0972-0.1840.06220.1821-0.03220.2192-27.41210.102620.283
30.01070.0205-0.00580.05470.02260.02250.0038-0.02880.0508-0.0527-0.0005-0.08610.0752-0.0089-0.04960.1191-0.16740.05570.0843-0.05570.184712.511742.135918.0645
40.02830.0333-0.00650.09660.04340.0319-0.01960.0053-0.069-0.15450.0369-0.02410.0397-0.0031-0.00770.203-0.13280.02960.1241-0.06990.171410.357243.127117.4567
50.07020.00310.0130.0697-0.01960.0086-0.0308-0.0312-0.046-0.06440.0397-0.00180.0662-0.070.03120.1443-0.070.02490.16240.00470.0894-18.68471.032514.1575
60.41890.11240.04350.19330.18020.3242-0.13740.03080.4074-0.04660.00660.1551-0.08040.0453-0.17870.078-0.0505-0.02190.1626-0.00560.19918.544771.493921.427
70.0724-0.0003-0.00260.142-0.05720.08560.0503-0.0264-0.02870.0591-0.055-0.11360.00310.0135-0.01850.1471-0.0512-0.01350.0670.00820.08910.309119.262616.1763
80.04540.02220.02960.4308-0.04710.03210.087-0.15640.0861-0.0476-0.05350.22920.0098-0.13160.19090.1448-0.05320.02520.1389-0.06570.11050.990351.61623.4745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 1 through 16)D1 - 16
2X-RAY DIFFRACTION2(chain 'E' and resid 1 through 16)E1 - 16
3X-RAY DIFFRACTION3(chain 'F' and resid 1 through 16)F1 - 16
4X-RAY DIFFRACTION4(chain 'G' and resid 1 through 16)G1 - 16
5X-RAY DIFFRACTION5(chain 'A' and resid 168 through 252)A168 - 252
6X-RAY DIFFRACTION6(chain 'B' and resid 168 through 250)B168 - 250
7X-RAY DIFFRACTION7(chain 'C' and resid 168 through 252)C168 - 252
8X-RAY DIFFRACTION8(chain 'H' and resid 168 through 252)H168 - 252

+
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