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- PDB-8a4i: Crystal structure of SALL4 zinc finger cluster 4 with AT-rich DNA -

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Basic information

Entry
Database: PDB / ID: 8a4i
TitleCrystal structure of SALL4 zinc finger cluster 4 with AT-rich DNA
Components
  • DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
  • Sal-like protein 4
KeywordsDNA BINDING PROTEIN / SALL4 / AT-rich DNA / Okihiro syndrome / transcription factor / stem cell
Function / homology
Function and homology information


Regulation of PTEN gene transcription / tissue development / embryonic limb morphogenesis / neural tube development / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / transcription factor binding / heterochromatin / neural tube closure ...Regulation of PTEN gene transcription / tissue development / embryonic limb morphogenesis / neural tube development / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / transcription factor binding / heterochromatin / neural tube closure / heart development / in utero embryonic development / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / nucleus / metal ion binding / 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 speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsWatson, J.A. / Pantier, R. / Jayachandran, U. / Chhatbar, K. / Alexander-Howden, B. / Kruusvee, V. / Prendecki, M. / Bird, A. / Cook, A.G.
Funding support United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Wellcome Trust200898 United Kingdom
Wellcome Trust107930 United Kingdom
Wellcome Trust092076 United Kingdom
Wellcome Trust203149 United Kingdom
European Research Council (ERC)EC 694295 Gen-EpixEuropean Union
CitationJournal: Life Sci Alliance / Year: 2023
Title: Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome.
Authors: Watson, J.A. / Pantier, R. / Jayachandran, U. / Chhatbar, K. / Alexander-Howden, B. / Kruusvee, V. / Prendecki, M. / Bird, A. / Cook, A.G.
History
DepositionJun 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Sal-like protein 4
J: Sal-like protein 4
K: Sal-like protein 4
L: Sal-like protein 4
A: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
B: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
E: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
F: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
G: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
H: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
C: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,14123
Polymers62,54512
Non-polymers59611
Water724
1
I: Sal-like protein 4
A: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
B: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7675
Polymers15,6363
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: Sal-like protein 4
L: Sal-like protein 4
C: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,28611
Polymers23,9524
Non-polymers3357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: Sal-like protein 4
E: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
F: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7675
Polymers15,6363
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')
H: DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3212
Polymers7,3212
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.026, 66.111, 77.938
Angle α, β, γ (deg.)73.040, 76.433, 76.140
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_1ens_2(chain "I" and (resid 882 or (resid 883 through 884...
d_2ens_2(chain "J" and (resid 882 or (resid 883 through 884...
d_3ens_2(chain "L" and (resid 882 or (resid 883 through 884...
d_4ens_2(chain "K" and (resid 882 through 894 or (resid 895...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1DGDCQ
d_21ens_1DGDCR
d_31ens_1DGDCW
d_41ens_1DGDCX
d_51ens_1DGDCS
d_61ens_1DGDCT
d_71ens_1DGDCU
d_81ens_1DGDCV
d_11ens_2CYSTHRA4 - 51
d_21ens_2CYSTHRJ4 - 51
d_31ens_2CYSTHRL5 - 52
d_41ens_2CYSTHRK3 - 50

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999646382242, -0.0257263732518, 0.00672786662022), (-0.000935915833234, -0.218812124489, -0.975766559295), (0.0265750734995, -0.975427807629, 0.218710670916)-12.9756756192, -0.107956880297, 0.315770893804
2given(-0.218178867821, -0.783866075478, 0.581336354747), (-0.270887461289, 0.620922628393, 0.735578053551), (-0.937559579415, 0.00301085762529, -0.347811687244)-5.7193931959, -35.536646093, -26.3202425185
3given(0.237642070305, -0.417864054634, 0.876878485462), (0.272226863557, -0.837911886452, -0.47307103621), (0.932426287263, 0.351131460265, -0.0853692944435)-2.74473416107, -32.0217155345, -14.2505498481
4given(-0.999960438388, -0.00253852030952, 0.00852511427668), (-0.00791749723052, 0.690818745244, -0.722984629475), (-0.00405399758228, -0.723023524607, -0.690811514068)0.103987760263, -6.37835313358, -41.1141530451
5given(0.999912207984, 0.0107698278748, -0.0077192702105), (-0.0125066996302, 0.574652357542, -0.818302053301), (-0.00437707543866, 0.818326755507, 0.574736602655)13.0127986975, -6.47000746926, -41.1353513489
6given(-0.232258071135, -0.747295049795, 0.622580353806), (-0.215181721821, 0.66370118837, 0.71637808394), (-0.948553116587, 0.0324166794758, -0.314954193344)4.97270776707, -26.011617819, 10.0864913076
7given(0.244681210801, -0.399872767368, 0.8833079163), (0.213751952625, -0.866340674299, -0.451402191848), (0.945749019471, 0.299258426738, -0.126503700328)8.12151568541, -22.8425622746, 22.5085260954
8given(-0.199437136637, -0.760425983769, 0.618043001529), (-0.235115206766, 0.649423702865, 0.723166435687), (-0.951286322869, -0.00108506484987, -0.308306916168)-5.75883418372, -35.572346257, -25.94134871
9given(0.240111708791, -0.336996436689, 0.910373422811), (0.290309659832, -0.869961611367, -0.398606442692), (0.926318880683, 0.360000272786, -0.111054648188)-2.27685433382, -32.256719371, -14.0442652515
10given(-0.998370143756, -0.0146280830711, 0.0551640756564), (-0.0509370236459, 0.664324712022, -0.745706441316), (-0.0257386029042, -0.747300940842, -0.663987069255)0.10423909061, -6.51399495124, -41.2454306039

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Components

#1: Protein
Sal-like protein 4 / Zinc finger protein SALL4


Mass: 8315.446 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sall4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BX22
#2: DNA chain
DNA (5'-D(*GP*AP*TP*AP*TP*TP*AP*AP*TP*AP*TP*C)-3')


Mass: 3660.428 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 50 mM MES pH 6.0, 20 % PEG 3350, 60 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2822 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.76→73.367 Å / Num. obs: 6179 / % possible obs: 0.7709 % / Redundancy: 3.28 % / Biso Wilson estimate: 39.02 Å2 / CC1/2: 0.8902 / Rmerge(I) obs: 0.452 / Rrim(I) all: 0.541 / Net I/σ(I): 3.122
Reflection shellResolution: 2.76→3.337 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1.903 / Num. unique obs: 309 / CC1/2: 0.669 / Rrim(I) all: 1.1 / % possible all: 0.2832

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL DNA

Resolution: 2.76→73.367 Å / SU ML: 0.3502 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.2427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2535 332 5.37 %
Rwork0.2473 5847 -
obs0.2476 6179 33.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.81 Å2
Refinement stepCycle: LAST / Resolution: 2.76→73.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 1944 11 4 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583612
X-RAY DIFFRACTIONf_angle_d0.8255301
X-RAY DIFFRACTIONf_chiral_restr0.0444603
X-RAY DIFFRACTIONf_plane_restr0.0058356
X-RAY DIFFRACTIONf_dihedral_angle_d28.39141344
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.72055848297
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.705708834336
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.681874362767
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.417581330648
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.563226600794
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.684432535158
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.723275419046
ens_2d_2IX-RAY DIFFRACTIONTorsion NCS0.726137099328
ens_2d_3IX-RAY DIFFRACTIONTorsion NCS0.772199713001
ens_2d_4IX-RAY DIFFRACTIONTorsion NCS0.746391726294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-3.480.3897320.3498454X-RAY DIFFRACTION5.32
3.48-73.3670.24313000.24095393X-RAY DIFFRACTION62.14

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