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- PDB-9lp4: Structural insights into the Tumor suppressor ZMYND11 reveal dive... -

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Basic information

Entry
Database: PDB / ID: 9lp4
TitleStructural insights into the Tumor suppressor ZMYND11 reveal diverse recognition mechanisms
Components
  • Early E1A protein
  • Zinc finger MYND domain-containing protein 11
KeywordsOXIDOREDUCTASE / tumor / zin finger
Function / homology
Function and homology information


symbiont-mediated suppression of host cGAS-STING signal transduction / histone H3K36me3 reader activity / DNA-templated viral transcription / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / : / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of signal transduction / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of canonical NF-kappaB signal transduction ...symbiont-mediated suppression of host cGAS-STING signal transduction / histone H3K36me3 reader activity / DNA-templated viral transcription / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / : / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of signal transduction / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway / symbiont-mediated activation of host apoptosis / transcription corepressor activity / chromosome / double-stranded DNA binding / defense response to virus / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / host cell nucleus / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Adenovirus early E1A protein / Early E1A protein / : / : / : / ZMYND11 protein coiled-coil / : / ZMYND11/ZMYD8, MYND zinc finger / : / SAM domain-containing protein 1, WH domain ...Adenovirus early E1A protein / Early E1A protein / : / : / : / 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
Early E1A protein / Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.96 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 zine figer structure and fuction of tumor suppressor ZMYND11
Authors: Bai, X. / Chen, Z.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
B: Early E1A protein
C: Zinc finger MYND domain-containing protein 11
D: Early E1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8888
Polymers31,6274
Non-polymers2624
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-72 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.136, 73.848, 116.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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: 14828.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND11, BRAM1, BS69 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15326
#2: Protein/peptide Early E1A protein / Early E1A 32 kDa protein


Mass: 985.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03254
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% MPD, 10%PEG4000,100 mM Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 198 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 7394 / % possible obs: 90.1 % / Redundancy: 7.3 % / CC1/2: 0.992 / Net I/σ(I): 16.6
Reflection shellResolution: 2.98→3.03 Å / Num. unique obs: 7036 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
PHENIX2.0_5761refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.96→36.92 Å / SU ML: 0.4395 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.3059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 386 5.22 %RANDOM
Rwork0.2081 7006 --
obs0.2096 7392 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.91 Å2
Refinement stepCycle: LAST / Resolution: 2.96→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 4 1 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082099
X-RAY DIFFRACTIONf_angle_d1.81232810
X-RAY DIFFRACTIONf_chiral_restr0.0796296
X-RAY DIFFRACTIONf_plane_restr0.0209360
X-RAY DIFFRACTIONf_dihedral_angle_d18.0545794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.390.30431100.27572147X-RAY DIFFRACTION90.39
3.39-4.270.2251430.20472365X-RAY DIFFRACTION99.68
4.27-36.920.22861330.1892494X-RAY DIFFRACTION98.72
Refinement TLS params.Method: refined / Origin x: -1.5338848066681 Å / Origin y: -18.670643648255 Å / Origin z: -25.359045815118 Å
111213212223313233
T0.34661524852773 Å20.030860820659815 Å20.016739145781753 Å2-0.33355250011223 Å20.021782586273386 Å2--0.3390511012821 Å2
L0.017857990860136 °2-0.015030095215737 °20.018148331462657 °2-0.017500913387916 °20.0024955069633837 °2--0.010464161526235 °2
S-0.054983814491969 Å °-0.010927665745392 Å °0.075809320002558 Å °0.016325291455004 Å °0.075050655813211 Å °-0.036804182541912 Å °0.053876513139235 Å °0.023601614711148 Å °0 Å °
Refinement TLS groupSelection details: all

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