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- PDB-7mla: Solution NMR structure of HDMX in complex with Zn and MCo-52-2 -

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Basic information

Entry
Database: PDB / ID: 7mla
TitleSolution NMR structure of HDMX in complex with Zn and MCo-52-2
Components
  • MCo-52-2
  • Protein Mdm4
KeywordsLIGASE / E3 Ligase / Zinc-binding protein / Cyclotide
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / negative regulation of protein catabolic process / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MDM4 / p53 negative regulator Mdm2/Mdm4 / 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 signature. / Zinc finger, RanBP2-type superfamily ...MDM4 / p53 negative regulator Mdm2/Mdm4 / 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 signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsRamirez, L.S. / Theophall, G. / Chaudhuri, D. / Camarero, J.C. / Shekhtman, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM08500606A1 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1P01HL146367 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM113636 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM135174 United States
CitationJournal: To Be Published
Title: Solution NMR structure of HDMX in complex with Zn and cyclotide 52-2
Authors: Chaudhuri, D. / Ramirez, L.S. / Theophall, G. / Shekhtman, A. / Camarero, J.C.
History
DepositionApr 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Mdm4
B: MCo-52-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5264
Polymers11,3952
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area970 Å2
ΔGint-9 kcal/mol
Surface area6980 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 7797.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Production host: Escherichia coli (E. coli) / References: UniProt: O15151
#2: Protein/peptide MCo-52-2


Mass: 3598.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-15N HSQC
141isotropic13D 1H-13C NOESY
151isotropic13D 1H-15N NOESY
161isotropic13D (H)CCH-TOCSY
171isotropic13D HBHA(CO)NH
181isotropic13D HN(CO)CA
191isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
1112isotropic12D 1H-13C HSQC
1122isotropic12D 1H-15N HSQC
1132isotropic13D 1H-13C NOESY
1142isotropic13D 1H-15N NOESY
1152isotropic13D (H)CCH-TOCSY
1162isotropic13D HNCA
1172isotropic13D CBCA(CO)NH
1182isotropic13D HN(CA)CB
1192isotropic13D HN(CO)CA
1201isotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.100 mM [U-100% 13C; U-100% 15N] Hdmx, 0.100 mM MCo-52-2, 90% H2O/10% D2O100 micromolar U-100% 13C, U-100% 15N HDMX, 100 micromolar natural abundance MCo-52-2 in 10 mM HEPES buffer, 100 nM zinc sulfate, 0.5 mM TCEP, 150 mM sodium chloride, 100 mM HMPA, pH 7.0, 298 K190% H2O/10% D2O
solution20.100 mM Hdmx, 0.100 mM [U-100% 13C; U-100% 15N] MCo-52-2, 90% H2O/10% D2O100 micromolar natural abundance HDMX, 100 micromolar U-100% 13C, U-100% 15N MCo-52-2 in 10 mM HEPES buffer, 100 nM zinc sulfate, 0.5 mM TCEP, 150 mM sodium chloride, 100 mM HMPA, pH 7.0, 298 K290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.100 mMHdmx[U-100% 13C; U-100% 15N]1
0.100 mMMCo-52-2natural abundance1
0.100 mMHdmxnatural abundance2
0.100 mMMCo-52-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.15 M / Label: 1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Ascend / Manufacturer: Bruker / Model: Ascend / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
YASARA20.4.24Krieger et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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