[English] 日本語
Yorodumi
- PDB-9c4t: menin mutant M327I in complex with MLL peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c4t
Titlemenin mutant M327I in complex with MLL peptide
Components
  • Histone-lysine N-methyltransferase 2A
  • Menin
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / Y-form DNA binding / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity ...negative regulation of DNA methylation-dependent heterochromatin formation / protein-cysteine methyltransferase activity / Y-form DNA binding / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / response to potassium ion / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / MLL1/2 complex / negative regulation of JNK cascade / definitive hemopoiesis / histone H3K4 methyltransferase activity / osteoblast development / anterior/posterior pattern specification / T-helper 2 cell differentiation / embryonic hemopoiesis / exploration behavior / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / R-SMAD binding / minor groove of adenine-thymine-rich DNA binding / cleavage furrow / MLL1 complex / negative regulation of cell cycle / negative regulation of protein phosphorylation / membrane depolarization / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / response to UV / four-way junction DNA binding / negative regulation of fibroblast proliferation / cellular response to transforming growth factor beta stimulus / spleen development / homeostasis of number of cells within a tissue / transcription repressor complex / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / : / response to gamma radiation / negative regulation of DNA-binding transcription factor activity / phosphoprotein binding / Post-translational protein phosphorylation / Deactivation of the beta-catenin transactivating complex / circadian regulation of gene expression / Formation of the beta-catenin:TCF transactivating complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / nuclear matrix / Transcriptional regulation of granulopoiesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / RUNX1 regulates transcription of genes involved in differentiation of HSCs / protein-containing complex assembly / double-stranded DNA binding / fibroblast proliferation / protein-macromolecule adaptor activity / methylation / chromosome, telomeric region / transcription cis-regulatory region binding / endoplasmic reticulum lumen / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Menin / Menin / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus ...Menin / Menin / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / PHD-finger / 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 profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Menin / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 Å
AuthorsClegg, B.D. / Cierpicki, T. / Grembecka, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)272561 United States
CitationJournal: To Be Published
Title: Menin mutant M327I in complex with MLL peptide
Authors: Clegg, B.D. / Cierpicki, T. / Grembecka, J.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Menin
B: Histone-lysine N-methyltransferase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6117
Polymers55,9552
Non-polymers6575
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-33 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.075, 80.456, 124.946
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Menin


Mass: 54552.184 Da / Num. of mol.: 1 / Mutation: M327I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, SCG2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00255
#2: Protein/peptide Histone-lysine N-methyltransferase 2A / C-terminal cleavage product of 180 kDa / p180


Mass: 1402.607 Da / Num. of mol.: 1 / Mutation: C5A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03164

-
Non-polymers , 5 types, 537 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 86122 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 28.13
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 4168 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000722data reduction
HKL-2000722data scaling
MOLREP11.0 / 22.07.2010phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.461→31.131 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.093 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 4372 5.081 %
Rwork0.1557 81677 -
all0.157 --
obs-86049 99.468 %
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: 17.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.377 Å20 Å2-0 Å2
2--0.851 Å20 Å2
3----1.229 Å2
Refinement stepCycle: LAST / Resolution: 1.461→31.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 44 533 4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163809
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.825538
X-RAY DIFFRACTIONr_angle_other_deg0.681.7458746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.028528
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.07951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07410656
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.38710184
X-RAY DIFFRACTIONr_chiral_restr0.1040.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
X-RAY DIFFRACTIONr_nbd_refined0.2360.2817
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23326
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22004
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2341
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3240.213
X-RAY DIFFRACTIONr_nbd_other0.2230.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.220
X-RAY DIFFRACTIONr_mcbond_it1.8731.4942018
X-RAY DIFFRACTIONr_mcbond_other1.8731.4942018
X-RAY DIFFRACTIONr_mcangle_it2.7372.6732551
X-RAY DIFFRACTIONr_mcangle_other2.7382.6752552
X-RAY DIFFRACTIONr_scbond_it2.8911.762043
X-RAY DIFFRACTIONr_scbond_other2.891.7612044
X-RAY DIFFRACTIONr_scangle_it4.3153.0912987
X-RAY DIFFRACTIONr_scangle_other4.3143.0912988
X-RAY DIFFRACTIONr_lrange_it5.6717.4274766
X-RAY DIFFRACTIONr_lrange_other5.66917.4284767
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
1.461-1.4990.2392950.24458370.24363030.9620.96497.2870.218
1.499-1.540.2293020.20857370.20961380.9670.97198.38710.181
1.54-1.5840.2063050.18256480.18460090.9730.97899.06810.155
1.584-1.6330.1812980.17254720.17258090.9780.9899.32860.146
1.633-1.6860.1862910.15853310.1656480.9780.98399.53970.133
1.686-1.7450.1883090.15651500.15854820.9770.98499.58040.132
1.745-1.8110.1942540.14949900.15252560.9770.98599.77170.129
1.811-1.8850.182800.14748180.14951020.980.98699.92160.127
1.885-1.9680.1922640.15245990.15448680.9770.98699.89730.135
1.968-2.0640.1872390.14944450.15146840.9770.9861000.138
2.064-2.1750.1652170.14242450.14344620.9830.9881000.132
2.175-2.3060.1632290.13240000.13342330.9840.9999.90550.125
2.306-2.4640.1671790.12937990.13139780.9820.9891000.124
2.464-2.660.1681800.14535400.14637200.9820.9871000.141
2.66-2.9120.2091620.14832900.15134520.9730.9861000.149
2.912-3.2520.1871620.16229800.16331420.9780.9841000.168
3.252-3.7490.1711470.1526300.15127770.9810.9871000.162
3.749-4.5750.1621090.1422660.14123750.9840.9881000.16
4.575-6.4010.217930.18118090.18219020.9790.9861000.206
6.401-31.1310.191570.19810910.19811550.9790.9899.39390.239

+
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