[English] 日本語
Yorodumi
- PDB-3mqm: Crystal Structure of the Bromodomain of human ASH1L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mqm
TitleCrystal Structure of the Bromodomain of human ASH1L
ComponentsProbable histone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / ASH1L / Ash1 / KIAA1420 / Absent small and homeotic disks protein 1 homolog / Lysine N-methyltransferase 2H / KMT2H / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / flagellated sperm motility / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of acute inflammatory response / decidualization / bicellular tight junction / single fertilization / negative regulation of MAPK cascade / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology domain ...ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Felletar, I. / Vollmar, M. / Chaikuad, A. / Krojer, T. / Canning, P. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Felletar, I. / Vollmar, M. / Chaikuad, A. / Krojer, T. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable histone-lysine N-methyltransferase ASH1L
B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)28,7512
Polymers28,7512
Non-polymers00
Water27015
1
A: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)14,3751
Polymers14,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)14,3751
Polymers14,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Probable histone-lysine N-methyltransferase ASH1L

B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)28,7512
Polymers28,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x-y,x+1,z-1/61
Buried area920 Å2
ΔGint-11 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.590, 69.590, 151.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA2433 - 24553 - 25
21GLUGLULYSLYSBB2433 - 24553 - 25
12LEULEULYSLYSAA2462 - 247332 - 43
22LEULEULYSLYSBB2462 - 247332 - 43
13ASNASNLEULEUAA2475 - 248645 - 56
23ASNASNLEULEUBB2475 - 248645 - 56
14LEULEULEULEUAA2488 - 249658 - 66
24LEULEULEULEUBB2488 - 249658 - 66
15THRTHRVALVALAA2497 - 250367 - 73
25THRTHRVALVALBB2497 - 250367 - 73
16GLUGLUGLUGLUAA2504 - 251874 - 88
26GLUGLUGLUGLUBB2504 - 251874 - 88
17LYSLYSPROPROAA2519 - 252689 - 96
27LYSLYSPROPROBB2519 - 252689 - 96
18VALVALVALVALAA2527 - 255397 - 123
28VALVALVALVALBB2527 - 255397 - 123

-
Components

#1: Protein Probable histone-lysine N-methyltransferase ASH1L / Absent small and homeotic disks protein 1 homolog / ASH1-like protein / huASH1 / Lysine N-methyltransferase 2H


Mass: 14375.469 Da / Num. of mol.: 2
Fragment: BROMODOMAIN of human ASH1L (UNP RESIDUES 2438:2564)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q9NR48, histone-lysine N-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M NaNO3 20% PEG3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.503
11-H-K, K, -L20.497
ReflectionResolution: 2.54→47.14 Å / Num. all: 13731 / Num. obs: 13718 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2022 / Rsym value: 0.76 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.54 Å38.68 Å
Translation2.54 Å38.68 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.54→47.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU B: 15.379 / SU ML: 0.153 / SU R Cruickshank DPI: 0.069 / SU Rfree: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 845 6.2 %RANDOM
Rwork0.204 ---
all0.207 13711 --
obs0.207 13682 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.69 Å2 / Biso mean: 66.426 Å2 / Biso min: 29.76 Å2
Baniso -1Baniso -2Baniso -3
1-29.52 Å20 Å20 Å2
2--29.52 Å20 Å2
3----59.04 Å2
Refinement stepCycle: LAST / Resolution: 2.54→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 0 15 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221952
X-RAY DIFFRACTIONr_bond_other_d0.0030.021284
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9742649
X-RAY DIFFRACTIONr_angle_other_deg0.92933142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71924.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87415316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3331510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
669TIGHT POSITIONAL0.030.05
732MEDIUM POSITIONAL0.060.5
669TIGHT THERMAL5.990.5
732MEDIUM THERMAL5.512
LS refinement shellResolution: 2.54→2.605 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 76 -
Rwork0.245 920 -
all-996 -
obs--98.22 %
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)
10.2906-0.3548-0.06230.52610.14160.8904-0.088-0.047-0.00390.03860.0221-0.02020.1221-0.12590.06590.1040.00860.02270.05190.02150.0475-39.453416.7122-2.0186
25.83865.51332.1715.5883-1.74862.19580.1203-0.0435-0.3842-1.4242-0.1111-0.75620.61410.0077-0.00910.30780.04940.12410.04740.01350.1582-28.2651.9246-1.1574
30.11580.1540.25831.47940.06490.6515-0.03330.00380.02620.1245-0.02530.074-0.06430.02990.05860.11830.02460.00330.06510.02280.0645-33.807922.11247.2425
40.77680.98990.93241.80681.36871.19520.0198-0.13830.0149-0.02190.0187-0.18970.0617-0.0826-0.03840.20350.01680.04620.1333-0.04850.1022-31.751512.330525.1483
50.3788-0.1058-0.2770.8383-0.4170.51260.2090.02810.2019-0.0510.0010.0904-0.1673-0.0536-0.210.13810.06180.06580.1337-0.06230.2056-47.308726.893934.2523
60.3798-0.4056-0.29010.79570.04781.175-0.0520.0576-0.0156-0.0904-0.0903-0.0149-0.0242-0.15170.14220.10440.0193-0.02120.062-0.00190.0613-39.16819.873522.7711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2431 - 2518
2X-RAY DIFFRACTION2A2519 - 2526
3X-RAY DIFFRACTION3A2527 - 2556
4X-RAY DIFFRACTION4B2431 - 2456
5X-RAY DIFFRACTION5B2457 - 2482
6X-RAY DIFFRACTION6B2483 - 2556

+
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