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- PDB-2vyr: Structure of human MDM4 N-terminal domain bound to a single domai... -

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Basic information

Entry
Database: PDB / ID: 2vyr
TitleStructure of human MDM4 N-terminal domain bound to a single domain antibody
Components
  • HUMAN SINGLE DOMAIN ANTIBODY
  • MDM4 PROTEIN
KeywordsIMMUNE SYSTEM / NUCLEUS / HUMAN MDM4 / ZINC-FINGER
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / negative regulation of protein catabolic process / Regulation of TP53 Degradation / ubiquitin-protein transferase activity / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / cellular response to hypoxia / Ub-specific processing proteases / protein ubiquitination / regulation of cell cycle / protein stabilization / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MDM4 / : / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others ...MDM4 / : / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYu, G.W. / Vaysburd, M. / Allen, M.D. / Settanni, G. / Fersht, A.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of Human Mdm4 N-Terminal Domain Bound to a Single-Domain Antibody.
Authors: Yu, G.W. / Vaysburd, M. / Allen, M.D. / Settanni, G. / Fersht, A.R.
History
DepositionJul 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MDM4 PROTEIN
B: MDM4 PROTEIN
C: MDM4 PROTEIN
D: MDM4 PROTEIN
E: HUMAN SINGLE DOMAIN ANTIBODY
F: HUMAN SINGLE DOMAIN ANTIBODY
G: HUMAN SINGLE DOMAIN ANTIBODY
H: HUMAN SINGLE DOMAIN ANTIBODY
I: HUMAN SINGLE DOMAIN ANTIBODY
J: HUMAN SINGLE DOMAIN ANTIBODY
K: HUMAN SINGLE DOMAIN ANTIBODY
L: HUMAN SINGLE DOMAIN ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,94416
Polymers181,56012
Non-polymers3844
Water13,547752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-298.1 kcal/mol
Surface area82640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.823, 115.200, 99.368
Angle α, β, γ (deg.)90.00, 104.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MDM4 PROTEIN / P53-BINDING PROTEIN MDM4 / MDM2-LIKE P53-BINDING PROTEIN / PROTEIN MDMX / DOUBLE MINUTE 4 PROTEIN / HUMAN MDM4


Mass: 11306.168 Da / Num. of mol.: 4 / Fragment: RESIDUES 16-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O15151
#2: Antibody
HUMAN SINGLE DOMAIN ANTIBODY


Mass: 17041.904 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: NON-BIOLOGICAL SEQUENCE, OBTAINED BY SELECTION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 50 %
Description: STRUCTURE WAS INITIALLY SOLVED USING MAD ON A SE- MET COMPLEX CONTAINING LABELLED MDMX. THE NATIVE STRUCTURE WAS SUBSEQUENTLY DETERMINED BY MOLECULAR REPLACEMENT
Crystal growpH: 7
Details: SE-MET: 20% PEG 3350, 0.2 M MGCL2, 1MM TRIS PH 7.0, 5MM B-ME, PROTEIN 10MG/ML. NATIVE: 1.6M AMMONIUM SULPHATE, 0.5M LITHIUM CHLORIDE, 1MM TRIS, PH 7.0, 5MM B-ME, PROTEIN 10MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.954
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 116657 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellHighest resolution: 2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→25 Å / SU ML: 0.32 / Phase error: 23.59 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.248 5655 5 %
Rwork0.207 --
obs-106975 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.385 Å2 / ksol: 0.346 e/Å3
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10471 0 20 752 11243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610768
X-RAY DIFFRACTIONf_angle_d0.95914565
X-RAY DIFFRACTIONf_dihedral_angle_d15.8763781
X-RAY DIFFRACTIONf_chiral_restr0.071535
X-RAY DIFFRACTIONf_plane_restr0.0041851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.25133400.23177115X-RAY DIFFRACTION98
2.0227-2.04650.28293840.23137171X-RAY DIFFRACTION98
2.0465-2.07150.28513450.23147164X-RAY DIFFRACTION98
2.0715-2.09770.27183690.22597157X-RAY DIFFRACTION98
2.0977-2.12530.27843970.22187147X-RAY DIFFRACTION98
2.1253-2.15440.27034100.21887133X-RAY DIFFRACTION98
2.1544-2.18510.28673580.22517204X-RAY DIFFRACTION98
2.1851-2.21770.28724220.21377198X-RAY DIFFRACTION98
2.2177-2.25230.24524020.20817103X-RAY DIFFRACTION98
2.2523-2.28920.25554280.20617152X-RAY DIFFRACTION98
2.2892-2.32870.27823780.21557109X-RAY DIFFRACTION98
2.3287-2.3710.28864110.21847243X-RAY DIFFRACTION98
2.371-2.41660.30463670.22297285X-RAY DIFFRACTION98
2.4166-2.46590.26933890.21657062X-RAY DIFFRACTION98
2.4659-2.51940.24043890.20737167X-RAY DIFFRACTION98
2.5194-2.5780.27993640.20757257X-RAY DIFFRACTION98
2.578-2.64240.26853880.21757120X-RAY DIFFRACTION98
2.6424-2.71370.23523800.20077134X-RAY DIFFRACTION98
2.7137-2.79350.25763620.20597230X-RAY DIFFRACTION98
2.7935-2.88350.26433960.21287097X-RAY DIFFRACTION98
2.8835-2.98640.28134190.22087207X-RAY DIFFRACTION98
2.9864-3.10580.23563160.21077211X-RAY DIFFRACTION98
3.1058-3.24680.26263890.20697092X-RAY DIFFRACTION98
3.2468-3.41760.23613220.19917201X-RAY DIFFRACTION98
3.4176-3.63110.2083700.19547158X-RAY DIFFRACTION98
3.6311-3.91050.22963340.1917175X-RAY DIFFRACTION98
3.9105-4.30230.20294060.18247103X-RAY DIFFRACTION97
4.3023-4.92070.20713690.17247009X-RAY DIFFRACTION96
4.9207-6.18390.21513520.19346728X-RAY DIFFRACTION92
6.1839-24.95830.22173540.18826817X-RAY DIFFRACTION93

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