[English] 日本語
Yorodumi
- PDB-5uml: CRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH 12-MER PEPTIDE IN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uml
TitleCRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH 12-MER PEPTIDE INHIBITOR M3
Components
  • PEPTIDE INHIBITOR M3
  • Protein Mdm4
KeywordsCell Cycle / Antitumor Protein/Inhibitor / Oncoprotein / Antitumor Protein-Inhibitor complex
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 / negative regulation of protein catabolic process ...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 / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / 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 / Ub-specific processing proteases / protein ubiquitination / regulation of cell cycle / 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 / Zinc finger, C3HC4 type (RING finger) ...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 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPazgier, M. / Gohain, N. / Tolbert, W.D.
CitationJournal: To Be Published
Title: Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for p53 activation
Authors: Pazgier, M. / Gohain, N. / Tolbert, W.D.
History
DepositionJan 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Source and taxonomy
Category: pdbx_audit_support / pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Oct 21, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein Mdm4
C: PEPTIDE INHIBITOR M3
B: Protein Mdm4
D: PEPTIDE INHIBITOR M3
E: Protein Mdm4
F: PEPTIDE INHIBITOR M3
G: Protein Mdm4
H: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)44,4728
Polymers44,4728
Non-polymers00
Water0
1
A: Protein Mdm4
C: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-13 kcal/mol
Surface area5660 Å2
MethodPISA
2
B: Protein Mdm4
D: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-14 kcal/mol
Surface area5750 Å2
MethodPISA
3
E: Protein Mdm4
F: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-15 kcal/mol
Surface area5550 Å2
MethodPISA
4
G: Protein Mdm4
H: PEPTIDE INHIBITOR M3


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers11,1182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area5640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.413, 88.027, 46.300
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 9575.293 Da / Num. of mol.: 4 / Fragment: residues 24-108 / Mutation: Q68A,Q69A,E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Protein/peptide
PEPTIDE INHIBITOR M3


Mass: 1542.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% (v/v) 2-Propanol ,70 mM Sodium acetate/ Hydrochloric acid pH 4.6, 140 mM Calcium chloride, 30% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 3592 / % possible obs: 49.8 % / Redundancy: 1.4 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.153 / Net I/σ(I): 2.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.364 / % possible all: 52.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RXZ

4rxz


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.788 / SU B: 96.288 / SU ML: 0.759 / Cross valid method: THROUGHOUT / ESU R Free: 1.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31526 180 5 %RANDOM
Rwork0.25791 ---
obs0.26079 3412 48.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å2-0 Å2-0.46 Å2
2--0.45 Å2-0 Å2
3----2.7 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 0 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193092
X-RAY DIFFRACTIONr_bond_other_d0.0030.022980
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9884170
X-RAY DIFFRACTIONr_angle_other_deg1.00536904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62624.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3191512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3413.4481504
X-RAY DIFFRACTIONr_mcbond_other0.343.4481503
X-RAY DIFFRACTIONr_mcangle_it0.6015.1681866
X-RAY DIFFRACTIONr_mcangle_other0.6015.1691867
X-RAY DIFFRACTIONr_scbond_it0.2363.4691588
X-RAY DIFFRACTIONr_scbond_other0.2363.4691589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4335.22305
X-RAY DIFFRACTIONr_long_range_B_refined1.54263.93510930
X-RAY DIFFRACTIONr_long_range_B_other1.54263.93310930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 9 -
Rwork0.337 278 -
obs--51.81 %
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)
11.8542-0.86680.02351.41151.02962.8743-0.06550.26970.13590.02350.01440.04330.1906-0.10150.05120.0946-0.0118-0.00010.10340.04780.02560.4448-20.66243.0204
21.58661.53850.56216.21682.70461.18650.1431-0.0752-0.0060.0492-0.20030.0950.016-0.08580.05720.12250.03530.0080.08060.02090.1117-5.5831-26.873412.4006
30.3707-0.54440.57161.9467-0.4344.2117-0.09720.14760.07510.02120.073-0.1373-0.00730.22610.02410.0744-0.054-0.0130.14890.03070.0277-23.2234-3.98013.0274
43.08840.39553.0462.8529-1.603911.3012-0.2147-0.07990.3182-0.0419-0.13860.07-0.3851-0.14580.35330.07860.02610.00070.0743-0.03860.131-17.08532.041613.5188
52.0671-0.36231.39550.7776-0.67593.6018-0.05090.03090.1547-0.02810.03630.11970.06630.26160.01450.0893-0.0081-0.03190.051-0.00990.07932.0073-0.962426.2136
62.9582-2.04032.89741.6302-1.31465.1662-0.1105-0.1898-0.0620.07810.1130.07990.0501-0.3297-0.00260.1284-0.0006-0.03720.1337-0.00610.1962-4.73524.808436.6648
72.5150.7628-0.64960.3118-0.70993.7297-0.14110.0791-0.0729-0.01670.0792-0.0459-0.0248-0.29420.06190.09120.05910.00580.0781-0.01410.1201-25.2071-23.62826.2208
80.2507-0.65760.35531.7513-0.74555.5586-0.0836-0.0102-0.06670.0349-0.04960.1845-0.1833-0.26170.13320.1280.0378-0.00440.20490.01590.2003-18.6474-29.363936.4819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 108
2X-RAY DIFFRACTION2C2 - 11
3X-RAY DIFFRACTION3B25 - 108
4X-RAY DIFFRACTION4D1 - 11
5X-RAY DIFFRACTION5E26 - 108
6X-RAY DIFFRACTION6F1 - 11
7X-RAY DIFFRACTION7G26 - 108
8X-RAY DIFFRACTION8H1 - 11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more