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- PDB-7x39: Structure of CIZ1 bound ERH -

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Basic information

Entry
Database: PDB / ID: 7x39
TitleStructure of CIZ1 bound ERH
ComponentsEnhancer of rudimentary homolog,Cip1-interacting zinc finger protein
KeywordsPROTEIN BINDING / ERH / CIZ1
Function / homology
Function and homology information


pyrimidine nucleoside metabolic process / methylosome / maintenance of protein location in nucleus / methyl-CpG binding / nucleobase-containing compound metabolic process / positive regulation of DNA-templated DNA replication initiation / cyclin binding / midbody / nucleic acid binding / cell cycle ...pyrimidine nucleoside metabolic process / methylosome / maintenance of protein location in nucleus / methyl-CpG binding / nucleobase-containing compound metabolic process / positive regulation of DNA-templated DNA replication initiation / cyclin binding / midbody / nucleic acid binding / cell cycle / RNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Cip1-interacting zinc finger protein / Enhancer of rudimentary signature. / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger ...Cip1-interacting zinc finger protein / Enhancer of rudimentary signature. / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Enhancer of rudimentary homolog / Cip1-interacting zinc finger protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWang, X. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Febs J. / Year: 2023
Title: Molecular basis for the recognition of CIZ1 by ERH.
Authors: Wang, X. / Xie, H. / Zhu, Z. / Zhang, J. / Xu, C.
History
DepositionFeb 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein
B: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein
C: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein
D: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein


Theoretical massNumber of molelcules
Total (without water)68,8004
Polymers68,8004
Non-polymers00
Water0
1
A: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein
B: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein


Theoretical massNumber of molelcules
Total (without water)34,4002
Polymers34,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-8 kcal/mol
Surface area13340 Å2
MethodPISA
2
C: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein
D: Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein


Theoretical massNumber of molelcules
Total (without water)34,4002
Polymers34,4002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.451, 48.668, 73.879
Angle α, β, γ (deg.)85.830, 75.080, 63.310
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Enhancer of rudimentary homolog,Cip1-interacting zinc finger protein / CDKN1A-interacting zinc finger protein 1 / Nuclear protein NP94 / Zinc finger protein 356


Mass: 17200.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CIZ1 fused with ERH / Source: (gene. exp.) Homo sapiens (human) / Gene: ERH, CIZ1, LSFR1, NP94, ZNF356 / Production host: Escherichia coli (E. coli) / References: UniProt: P84090, UniProt: Q9ULV3

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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: 2 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-tris propane pH 9.0, 20% v/v Jeffamine ED-2001 pH 7.0, 6% glycerol

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Data collection

DiffractionMean temperature: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.85→43.43 Å / Num. obs: 12023 / % possible obs: 96.6 % / Redundancy: 3.6 % / CC1/2: 0.985 / Net I/σ(I): 5.4
Reflection shellResolution: 2.85→3 Å / Num. measured obs: 12045 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ7

1wz7


Resolution: 2.85→38.078 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 694 5.77 %
Rwork0.2181 11329 -
obs0.221 12023 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.65 Å2 / Biso mean: 49.1906 Å2 / Biso min: 24.42 Å2
Refinement stepCycle: final / Resolution: 2.85→38.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 0 0 3828
Num. residues----479
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8501-3.070.32521470.2786225896
3.07-3.37880.33631270.2657222195
3.3788-3.86730.29071300.2263228998
3.8673-4.87080.22591440.1861228096
4.8708-38.0780.241460.1954228198
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)
10.72410.48380.02360.9008-0.15920.4883-0.04950.0199-0.11630.04040.0061-0.0092-0.05890.019600.23510.0129-0.02010.2717-0.00010.397-19.61296.081-17.1926
20.33910.0201-0.07230.17510.05320.03130.20660.0799-0.5219-0.574-0.231-0.26560.27870.01590.00060.3222-0.02740.0520.27940.02430.5386-15.431520.7734-12.0624
31.0409-0.25030.27050.7490.1740.10090.05610.16370.15480.0279-0.07370.01950.1049-0.072800.2787-0.03740.03110.32230.01910.3352-19.1303-19.9436-24.755
40.1424-0.15830.06040.1016-0.05630.14880.1901-0.0889-0.6649-0.2897-0.2115-0.25470.36520.329400.2764-0.0327-0.0150.44360.01820.3792-13.6542-32.3921-33.727
50.25640.05850.17960.4677-0.10310.94250.11170.05750.2220.0074-0.0168-0.2677-0.01590.020200.48160.0342-0.01930.4413-0.01250.3712-22.690616.767719.8055
60.0981-0.02950.004-0.02460.01630.13540.1802-0.44320.55850.2746-0.35730.29270.29580.4654-0.00130.8675-0.0702-0.09990.9802-0.02630.5283-20.652932.212618.365
70.30480.22840.04420.5614-0.2870.8645-0.1373-0.070.01260.1210.05580.0173-0.158-0.13870.00010.47960.0059-0.02360.36120.00590.3882-20.5417-8.29819.6747
80.03660.032-0.00070.0261-0.02570.0170.10850.1982-0.0286-0.36580.22090.00230.584-0.63290.00030.68850.1255-0.06230.67760.08010.3981-26.0985-20.61540.7988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 100 )A0 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 156 )A132 - 156
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 100 )B1 - 100
4X-RAY DIFFRACTION4chain 'B' and (resid 134 through 150 )B134 - 150
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 100 )C1 - 100
6X-RAY DIFFRACTION6chain 'C' and (resid 134 through 150 )C134 - 150
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 100 )D1 - 100
8X-RAY DIFFRACTION8chain 'D' and (resid 134 through 150 )D134 - 150

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