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- PDB-8xu6: Study on zinc finger structure and function of tumor suppressor Z... -

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Basic information

Entry
Database: PDB / ID: 8xu6
TitleStudy on zinc finger structure and function of tumor suppressor ZMYND11
ComponentsZinc finger MYND domain-containing protein 11
KeywordsANTITUMOR PROTEIN / tumor / zinc finger
Function / homology
Function and homology information


histone H3K36me3 reader activity / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / : / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromosome / double-stranded DNA binding ...histone H3K36me3 reader activity / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / : / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromosome / double-stranded DNA binding / defense response to virus / negative regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / ZMYND11 protein coiled-coil / : / ZMYND11/ZMYD8, MYND zinc finger / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger MYND-type signature. ...: / : / : / ZMYND11 protein coiled-coil / : / ZMYND11/ZMYD8, MYND zinc finger / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.628 Å
AuthorsBai, X. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Study on zinc finger structure and function of tumor suppressor ZMYND11
Authors: Bai, X. / Chen, Z.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5153
Polymers6,3841
Non-polymers1312
Water45025
1
A: Zinc finger MYND domain-containing protein 11
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)39,09118
Polymers38,3076
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area9560 Å2
ΔGint-314 kcal/mol
Surface area16310 Å2
MethodPISA
2
A: Zinc finger MYND domain-containing protein 11
hetero molecules

A: Zinc finger MYND domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0306
Polymers12,7692
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
Buried area1680 Å2
ΔGint-95 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.022, 55.022, 74.411
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-317-

HOH

31A-319-

HOH

41A-321-

HOH

51A-322-

HOH

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Components

#1: Protein Zinc finger MYND domain-containing protein 11 / Adenovirus 5 E1A-binding protein / Bone morphogenetic protein receptor-associated molecule 1 / Protein BS69


Mass: 6384.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND11, BRAM1, BS69 / Production host: prokaryote coculture (bacteria) / References: UniProt: Q15326
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40 % v/v 2-Methyl-2,4-pentanediol,100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 198 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.628→47.76 Å / Num. obs: 8809 / % possible obs: 99.88 % / Redundancy: 19 % / CC1/2: 0.997 / Net I/σ(I): 73.4
Reflection shellResolution: 1.63→1.66 Å / Num. unique obs: 2301 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.628→47.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.19 / SU B: 6.081 / SU ML: 0.086 / Average fsc free: 0.8967 / Average fsc work: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.087
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 430 4.881 %RANDOM
Rwork0.1809 8379 --
all0.183 ---
obs-8809 99.447 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.074 Å2
Baniso -1Baniso -2Baniso -3
1-1.102 Å20.551 Å20 Å2
2--1.102 Å2-0 Å2
3----3.576 Å2
Refinement stepCycle: LAST / Resolution: 1.628→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms422 0 0 25 447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012433
X-RAY DIFFRACTIONr_bond_other_d0.0010.017368
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.624585
X-RAY DIFFRACTIONr_angle_other_deg0.6191.563850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.106553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.65220.45522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.941563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.629153
X-RAY DIFFRACTIONr_chiral_restr0.1020.251
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02106
X-RAY DIFFRACTIONr_nbd_refined0.1910.274
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.2325
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2201
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.27
X-RAY DIFFRACTIONr_nbd_other0.1390.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.28
X-RAY DIFFRACTIONr_mcbond_it6.4434.464215
X-RAY DIFFRACTIONr_mcbond_other6.3134.45214
X-RAY DIFFRACTIONr_mcangle_it7.9076.678267
X-RAY DIFFRACTIONr_mcangle_other7.8946.691268
X-RAY DIFFRACTIONr_scbond_it7.2794.857218
X-RAY DIFFRACTIONr_scbond_other7.2624.865219
X-RAY DIFFRACTIONr_scangle_it8.4287.036318
X-RAY DIFFRACTIONr_scangle_other8.4247.037318
X-RAY DIFFRACTIONr_lrange_it8.03349.551460
X-RAY DIFFRACTIONr_lrange_other8.06149.688461
X-RAY DIFFRACTIONr_rigid_bond_restr3.7073800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.628-1.6710.335270.2995920.36320.6190.69397.9430.231
1.671-1.7160.311270.2335880.2366180.770.80999.51460.187
1.716-1.7660.23250.1875750.1896000.90.8771000.14
1.766-1.820.242290.2055590.2075880.890.8991000.16
1.82-1.880.213270.1745380.1755650.9070.9341000.147
1.88-1.9460.206230.1735300.1755530.9470.9241000.144
1.946-2.0190.232300.1645100.1685400.9260.9431000.144
2.019-2.1010.287280.154810.1575090.9190.9561000.132
2.101-2.1950.164240.1424740.1434990.9560.95499.79960.124
2.195-2.3010.302240.1454510.1524750.9170.9481000.131
2.301-2.4260.247320.1734210.1784530.9180.9441000.157
2.426-2.5720.259190.1654160.1684350.8970.9531000.16
2.572-2.7490.286220.1613910.1674130.9390.9551000.16
2.749-2.9690.278210.183610.1853820.9220.9481000.184
2.969-3.2510.26210.1833390.1883600.930.941000.185
3.251-3.6330.284130.1693120.1743250.9580.961000.183
3.633-4.190.18140.1482860.153000.9650.9761000.172
4.19-5.1220.105150.1652380.162550.9830.9799.21570.197
5.122-7.2030.2550.1852000.1872110.9760.96797.15640.231
7.203-47.650.31740.4431170.4391420.8610.83285.21130.789

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