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- PDB-4ii1: Crystal structure of the zinc finger of ZGPAT -

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Basic information

Entry
Database: PDB / ID: 4ii1
TitleCrystal structure of the zinc finger of ZGPAT
ComponentsZinc finger CCCH-type with G patch domain-containing protein
KeywordsTRANSCRIPTION / transcription regulation / structural genomics consortium / SGC
Function / homology
Function and homology information


negative regulation of epidermal growth factor-activated receptor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm ...negative regulation of epidermal growth factor-activated receptor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / plasma membrane
Similarity search - Function
SH3 type barrels. - #1190 / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type ...SH3 type barrels. - #1190 / E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Zinc finger CCCH-type with G patch domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsBian, C. / Tempel, W. / Dong, A. / Chao, X. / Fu, M. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. ...Bian, C. / Tempel, W. / Dong, A. / Chao, X. / Fu, M. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the zinc finger of ZGPAT
Authors: Bian, C. / Tempel, W. / Dong, A. / Chao, X. / Fu, M. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger CCCH-type with G patch domain-containing protein
B: Zinc finger CCCH-type with G patch domain-containing protein
C: Zinc finger CCCH-type with G patch domain-containing protein
D: Zinc finger CCCH-type with G patch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,37327
Polymers75,1114
Non-polymers26223
Water00
1
A: Zinc finger CCCH-type with G patch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8437
Polymers18,7781
Non-polymers656
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zinc finger CCCH-type with G patch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8436
Polymers18,7781
Non-polymers655
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Zinc finger CCCH-type with G patch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8435
Polymers18,7781
Non-polymers654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Zinc finger CCCH-type with G patch domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8439
Polymers18,7781
Non-polymers658
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.170, 87.070, 76.570
Angle α, β, γ (deg.)90.000, 95.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Zinc finger CCCH-type with G patch domain-containing protein / G patch domain-containing protein 6 / Zinc finger CCCH domain-containing protein 9 / Zinc finger ...G patch domain-containing protein 6 / Zinc finger CCCH domain-containing protein 9 / Zinc finger and G patch domain-containing protein


Mass: 18777.736 Da / Num. of mol.: 4 / Fragment: UNP residues 119-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZGPAT, GPATC6, GPATCH6, KIAA1847, ZC3H9, ZC3HDC9, ZIP / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8N5A5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2 M sodium citrate, 5% MPD, 0.1 M sodium HEPES, 3 molar equivalents of H3K4me3 peptide., pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.28292 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28292 Å / Relative weight: 1
ReflectionResolution: 2.65→37.8 Å / Num. obs: 20804 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.802 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.9461.946400151998.3
2.72-2.790.7442.316311148198.7
2.79-2.870.5383.116160144498.8
2.87-2.960.3924.026012141298.9
2.96-3.060.3174.845979140598.7
3.06-3.170.2256.445521128998.8
3.17-3.290.1668.435468128899.2
3.29-3.420.11710.795248123799.5
3.42-3.570.10412.444979117598.7
3.57-3.750.07615.214707112698.8
3.75-3.950.06118.164585109399.3
3.95-4.190.04920.894267101799
4.19-4.480.04623.12399896599.3
4.48-4.840.04224.19370790499.3
4.84-5.30.04325.21336181899.4
5.3-5.930.04824.41307975799.5
5.93-6.840.05124.42263266498.7
6.84-8.380.04826.23220555597.2
8.38-11.850.04228.22166543197.1
11.850.03727.6481922486.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
SHARPphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.65→37.8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.8855 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.494 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DM, resolve, refmac, buccaneer, arp/warp atom update, PARROT, PHASER were also used for phase improvement and model building/refinement. COOT was used for interactive model re-building and ...Details: DM, resolve, refmac, buccaneer, arp/warp atom update, PARROT, PHASER were also used for phase improvement and model building/refinement. COOT was used for interactive model re-building and model geometry was validated on the MOLPROBITY server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 985 4.74 %THIN SHELLS (SFTOOLS)
Rwork0.2085 ---
obs0.2102 20787 98.76 %-
Displacement parametersBiso max: 163.14 Å2 / Biso mean: 66.9971 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-9.6709 Å20 Å24.6329 Å2
2---12.7657 Å20 Å2
3---3.0948 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: LAST / Resolution: 2.65→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 23 0 3970
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1225SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes622HARMONIC5
X-RAY DIFFRACTIONt_it4054HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion530SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4025SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4054HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg5540HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.52
LS refinement shellResolution: 2.65→2.79 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2388 147 4.9 %
Rwork0.2299 2850 -
all0.2304 2997 -
obs--98.76 %

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