[English] 日本語
Yorodumi
- PDB-7y3i: Structure of DNA bound SALL4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y3i
TitleStructure of DNA bound SALL4
Components
  • (DNA (12-mer)) x 2
  • Sal-like protein 4
KeywordsDNA/DNA BINDING PROTEIN / SALL4 / zinc finger / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / inner cell mass cell proliferation / ventricular septum development / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / inner cell mass cell proliferation / ventricular septum development / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Sal-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsRu, W. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif.
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif
Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C.
History
DepositionJun 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: DNA (12-mer)
K: DNA (12-mer)
G: DNA (12-mer)
H: DNA (12-mer)
A: Sal-like protein 4
B: Sal-like protein 4
C: Sal-like protein 4
D: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34914
Polymers48,9578
Non-polymers3926
Water2,630146
1
L: DNA (12-mer)
K: DNA (12-mer)
B: Sal-like protein 4
D: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6757
Polymers24,4784
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-33 kcal/mol
Surface area8720 Å2
MethodPISA
2
G: DNA (12-mer)
H: DNA (12-mer)
A: Sal-like protein 4
C: Sal-like protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6757
Polymers24,4784
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-35 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.975, 69.197, 110.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain DNA (12-mer)


Mass: 3670.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (12-mer)


Mass: 3652.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Sal-like protein 4 / Zinc finger protein 797 / Zinc finger protein SALL4


Mass: 8577.798 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SALL4, ZNF797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJQ4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-tris, pH 6.5, 25% w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→48.98 Å / Num. obs: 14297 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.996 / Net I/σ(I): 9.9
Reflection shellResolution: 2.45→2.63 Å / Num. unique obs: 14297 / CC1/2: 0.739

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→43.127 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 678 4.74 %
Rwork0.1942 13619 -
obs0.1966 14297 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.15 Å2 / Biso mean: 35.9218 Å2 / Biso min: 18.04 Å2
Refinement stepCycle: final / Resolution: 2.45→43.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 984 6 146 2357
Biso mean--32.87 34.27 -
Num. residues----208
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4501-2.63920.34731200.25422669100
2.6392-2.90480.29681370.25032694100
2.9048-3.32490.24791320.20362686100
3.3249-4.18850.20021490.1628271399
4.1885-43.1270.23581400.1807285799
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)
10.2614-0.19710.02150.79040.33840.1960.0603-0.00410.03170.01890.22890.3026-0.0313-0.11050.00070.33180.0226-0.04220.30940.08590.273615.1392-0.961622.4278
21.241-0.1841-0.30641.46580.71130.3736-0.06360.28550.13920.5196-0.03760.2358-0.26630.3418-0.00130.2606-0.0003-0.0320.30720.0670.33317.4056-1.419723.4245
30.6651-0.5019-0.31910.6070.55680.57930.07270.0587-0.13720.0001-0.02250.1293-0.01870.17010.00010.2698-0.01270.0410.31240.05010.202939.40780.39690.7345
40.946-0.0890.28940.76990.50290.46830.00910.0285-0.1433-0.24160.13190.06240.18320.04310.00020.2854-0.01590.00650.270.05880.228141.47010.5634-0.2975
50.45630.34270.10971.5376-0.96420.9119-0.1922-0.19020.00430.1780.08460.1405-0.0647-0.0485-0.00010.22820.0082-0.01730.27260.01770.306241.75829.6523.7671
60.20470.4665-0.42732.1492-0.67311.010.07270.06690.0001-0.2171-0.06830.28480.1002-0.104200.2384-0.0028-0.02140.1918-0.01610.247517.7247-10.754219.9738
70.31190.1452-0.17220.33940.10050.2109-0.0945-0.1361-0.1258-0.2213-0.040.0463-0.07190.0158-0.00090.34170.00120.04820.3282-0.00320.325544.99-7.3329-13.2709
80.2236-0.00220.06370.37070.08280.3051-0.3692-0.2823-0.01110.1208-0.00930.3035-0.1419-0.16840.00010.3380.0102-0.01680.3526-0.010.378716.319110.67335.4541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'L' and resid 1 through 12)L1 - 12
2X-RAY DIFFRACTION2(chain 'K' and resid 0 through 11)K0 - 11
3X-RAY DIFFRACTION3(chain 'G' and resid 1 through 12)G1 - 12
4X-RAY DIFFRACTION4(chain 'H' and resid 1 through 12)H1 - 12
5X-RAY DIFFRACTION5(chain 'A' and resid 868 through 921)A868 - 921
6X-RAY DIFFRACTION6(chain 'B' and resid 869 through 921)B869 - 921
7X-RAY DIFFRACTION7(chain 'C' and resid 895 through 921)C895 - 921
8X-RAY DIFFRACTION8(chain 'D' and resid 896 through 921)D896 - 921

+
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