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- PDB-7k7t: Crystal structure of human MORC4 ATPase-CW in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7k7t
TitleCrystal structure of human MORC4 ATPase-CW in complex with AMPPNP
ComponentsIsoform 3 of MORC family CW-type zinc finger protein 4
KeywordsTRANSCRIPTION / Chromatin / Histone H3K4me3 / DNA interaction
Function / homology
Function and homology information


methylated histone binding / ATP hydrolysis activity / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MICRORCHIDIA ATPase family / Morc, S5 domain 2-like / Morc6 ribosomal protein S5 domain 2-like / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MORC family CW-type zinc finger protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsKlein, B.J. / Tencer, A.H. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2020
Title: Molecular mechanism of the MORC4 ATPase activation.
Authors: Tencer, A.H. / Cox, K.L. / Wright, G.M. / Zhang, Y. / Petell, C.J. / Klein, B.J. / Strahl, B.D. / Black, J.C. / Poirier, M.G. / Kutateladze, T.G.
History
DepositionSep 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of MORC family CW-type zinc finger protein 4
B: Isoform 3 of MORC family CW-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6728
Polymers104,4802
Non-polymers1,1926
Water54030
1
A: Isoform 3 of MORC family CW-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8364
Polymers52,2401
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 3 of MORC family CW-type zinc finger protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8364
Polymers52,2401
Non-polymers5963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.424, 109.934, 70.390
Angle α, β, γ (deg.)90.000, 95.952, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 29 through 68 or resid 70...
d_2ens_1(chain "B" and (resid 29 through 68 or resid 70...
d_1ens_2chain "A" and resid 503
d_2ens_2chain "B" and resid 503

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA1 - 40
d_12ens_1THRASPA42 - 80
d_13ens_1PROLEUA83 - 122
d_14ens_1CYSPROA124 - 136
d_15ens_1ASNILEA138 - 142
d_16ens_1SERARGA144 - 184
d_17ens_1SERASPA191 - 198
d_18ens_1TYRASPA200 - 206
d_19ens_1LEUMETA208 - 224
d_110ens_1PROMETA226 - 241
d_111ens_1ALACYSA243 - 271
d_112ens_1PHECYSA275 - 294
d_113ens_1GLYLYSA297 - 322
d_114ens_1TYRTRPA324 - 339
d_115ens_1GLUTHRA341 - 343
d_116ens_1VALLEUA345 - 362
d_117ens_1GLYGLYA364
d_118ens_1PROALAA369 - 370
d_119ens_1TRPCYSA372 - 374
d_120ens_1TYRASNA376 - 377
d_121ens_1CYSGLUA383 - 388
d_21ens_1GLYALAB1 - 40
d_22ens_1THRASPB42 - 80
d_23ens_1PROLEUB82 - 121
d_24ens_1CYSPROB123 - 135
d_25ens_1ASNILEB140 - 144
d_26ens_1SERARGB147 - 187
d_27ens_1SERASPB189 - 196
d_28ens_1TYRASPB198 - 204
d_29ens_1LEUMETB206 - 222
d_210ens_1PROMETB224 - 239
d_211ens_1ALACYSB241 - 289
d_212ens_1GLYLYSB292 - 317
d_213ens_1TYRTRPB320 - 335
d_214ens_1GLUTHRB337 - 339
d_215ens_1VALLEUB341 - 358
d_216ens_1GLYGLYB360
d_217ens_1PROALAB367 - 368
d_218ens_1TRPCYSB370 - 372
d_219ens_1TYRASNB374 - 375
d_220ens_1CYSGLUB382 - 387
d_11ens_2ZNZNC
d_12ens_2MGMGD
d_13ens_2ANPANPE
d_21ens_2ZNZNF
d_22ens_2MGMGG
d_23ens_2ANPANPH

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein Isoform 3 of MORC family CW-type zinc finger protein 4 / Zinc finger CW-type coiled-coil domain protein 2 / Zinc finger CW-type domain protein 4


Mass: 52239.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORC4, ZCW4, ZCWCC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TE76
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes 7.5, 20% Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2782 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 16000 / % possible obs: 94.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.08 Å2 / Rpim(I) all: 0.079 / Net I/σ(I): 10.1
Reflection shellResolution: 2.94→3.05 Å / Num. unique obs: 1280 / Rpim(I) all: 0.285 / % possible all: 75.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O1E

6o1e


Resolution: 2.94→47.11 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.4791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1517 10.04 %
Rwork0.237 13589 -
obs0.2397 15106 89.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.66 Å2
Refinement stepCycle: LAST / Resolution: 2.94→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 66 30 6329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326431
X-RAY DIFFRACTIONf_angle_d0.58788672
X-RAY DIFFRACTIONf_chiral_restr0.0439957
X-RAY DIFFRACTIONf_plane_restr0.00371085
X-RAY DIFFRACTIONf_dihedral_angle_d19.40352405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.891211082715
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.183331771398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.040.281596854X-RAY DIFFRACTION62.21
3.04-3.140.31711140.28641026X-RAY DIFFRACTION74.75
3.15-3.270.32651320.29061168X-RAY DIFFRACTION84.75
3.27-3.420.31721370.2721242X-RAY DIFFRACTION90.84
3.42-3.60.28091400.25791253X-RAY DIFFRACTION91.05
3.6-3.820.26991490.24391326X-RAY DIFFRACTION94.79
3.83-4.120.26161420.22881294X-RAY DIFFRACTION93.49
4.12-4.530.23911460.2051334X-RAY DIFFRACTION97.37
4.54-5.190.21281530.1981338X-RAY DIFFRACTION95.52
5.19-6.540.26551520.2371353X-RAY DIFFRACTION97.16
6.54-47.110.25531560.21891401X-RAY DIFFRACTION99.05
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)
10.072723069671-0.0286479342475-0.0005796121782870.0445104005288-0.03455914203760.04398878967170.248325943856-0.1081339457960.0928825648656-0.187054417627-0.2211922623220.03898974430540.1822334262620.02153858842132.8913741788E-120.1636547517150.0425877327024-0.0150653336970.142688013707-0.00734207965580.161855735866-8.27336807571-3.39826344589-17.1087865419
20.0140829156833-0.00130779733840.01690864314670.0537552541694-0.01219957441740.03881531424290.113958289910.01720774875970.1291860930360.03731392600090.002128223984720.05562272431890.08756974208-0.07608284493867.99822728893E-110.1347992665040.009633504766090.02398482206680.1370059443960.02324086622560.144500780922-14.067541611829.8973748875-21.7656271658
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 29 through 471)AA29 - 4711 - 390
22(chain 'B' and resid 29 through 469)BB29 - 4691 - 387

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