[English] 日本語
Yorodumi
- PDB-6e29: Crystal structure of Myceliophteria_thermophila Cps50 (Swd1) beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+29
TitleCrystal structure of Myceliophteria_thermophila Cps50 (Swd1) beta-propeller domain
ComponentsSWD1-like protein
KeywordsPROTEIN BINDING / histone / epigenetics / COMPASS / histone H3 Lys-4 methylation / MLL1 / SET1
Function / homology
Function and homology information


Set1C/COMPASS complex
Similarity search - Function
Retinoblastoma-binding protein 5/Swd1 / : / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.818 Å
AuthorsJoshi, M. / Yang, Y. / Brunzelle, J.S. / Couture, J.F.
CitationJournal: Cell / Year: 2018
Title: Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex.
Authors: Qianhui Qu / Yoh-Hei Takahashi / Yidai Yang / Hongli Hu / Yan Zhang / Joseph S Brunzelle / Jean-Francois Couture / Ali Shilatifard / Georgios Skiniotis /
Abstract: The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity ...The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 22, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: SWD1-like protein
A: SWD1-like protein
B: SWD1-like protein
C: SWD1-like protein


Theoretical massNumber of molelcules
Total (without water)156,4454
Polymers156,4454
Non-polymers00
Water12,178676
1
A: SWD1-like protein


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SWD1-like protein


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SWD1-like protein


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SWD1-like protein


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.784, 88.900, 124.319
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
SWD1-like protein


Mass: 39111.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Gene: MYCTH_2294520 / Production host: Escherichia coli (E. coli) / References: UniProt: G2Q1Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium citrate, 22% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.07812 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.818→45.1 Å / Num. obs: 116058 / % possible obs: 92 % / Redundancy: 6.9 % / Rsym value: 0.077 / Net I/σ(I): 13.8
Reflection shellResolution: 1.818→1.86 Å / Rsym value: 0.075

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H13

2h13


Resolution: 1.818→45.026 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 5197 4.9 %
Rwork0.1676 --
obs0.1701 105994 90.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.818→45.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10111 0 0 676 10787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410596
X-RAY DIFFRACTIONf_angle_d1.31614445
X-RAY DIFFRACTIONf_dihedral_angle_d3.5758688
X-RAY DIFFRACTIONf_chiral_restr0.0921618
X-RAY DIFFRACTIONf_plane_restr0.0091849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8182-1.83890.32271980.25773644X-RAY DIFFRACTION100
1.8389-1.86050.33112040.24223669X-RAY DIFFRACTION100
1.8605-1.88320.31781820.22843681X-RAY DIFFRACTION100
1.8832-1.9070.28611620.21273183X-RAY DIFFRACTION98
1.907-1.93210.2239370.1952939X-RAY DIFFRACTION97
1.9321-1.95860.23081760.17493650X-RAY DIFFRACTION100
1.9586-1.98660.25342000.17743721X-RAY DIFFRACTION100
1.9866-2.01620.26931950.17593607X-RAY DIFFRACTION100
2.0162-2.04770.22971900.17413649X-RAY DIFFRACTION100
2.0477-2.08130.2691630.18231345X-RAY DIFFRACTION36
2.0813-2.11720.23462000.17253665X-RAY DIFFRACTION99
2.1172-2.15570.24462040.16583660X-RAY DIFFRACTION100
2.1557-2.19710.23411580.17263685X-RAY DIFFRACTION100
2.1971-2.2420.24191680.17172948X-RAY DIFFRACTION98
2.242-2.29070.1956740.17911835X-RAY DIFFRACTION98
2.2907-2.3440.26271610.17573606X-RAY DIFFRACTION98
2.344-2.40260.24871840.18763631X-RAY DIFFRACTION97
2.4026-2.46760.2431620.18733469X-RAY DIFFRACTION94
2.4676-2.54020.24521870.19133626X-RAY DIFFRACTION99
2.5402-2.62220.27772100.19123678X-RAY DIFFRACTION100
2.6222-2.71590.24541700.193705X-RAY DIFFRACTION100
2.7159-2.82460.27591910.1953695X-RAY DIFFRACTION100
2.8246-2.95310.23961950.18753663X-RAY DIFFRACTION100
2.9531-3.10880.23881940.18373696X-RAY DIFFRACTION99
3.1088-3.30350.23132050.17153669X-RAY DIFFRACTION99
3.3035-3.55850.19211910.15153191X-RAY DIFFRACTION86
3.5585-3.91640.18851760.13833204X-RAY DIFFRACTION87
3.9164-4.48270.14311920.1243654X-RAY DIFFRACTION98
4.4827-5.6460.13861730.12993640X-RAY DIFFRACTION97
5.646-45.03940.21471950.18523789X-RAY DIFFRACTION99
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)
14.15670.4137-1.13734.0421-1.40055.05750.0232-0.03880.067-0.18090.0158-0.0490.21570.0274-0.11150.18680.00520.00820.17-0.03210.159724.056421.819467.0798
22.92321.02971.38133.2051.02842.2634-0.0391-0.13550.2161-0.0313-0.0940.327-0.1444-0.16340.12170.17070.01940.030.1419-0.01640.173511.982225.409662.6276
33.05450.14070.32783.42250.17543.4465-0.02370.0313-0.1369-0.1307-0.07730.54430.2195-0.36890.05890.1777-0.0399-0.01230.2011-0.00950.24692.288412.319152.4265
44.3954-1.14690.63883.0205-0.82163.86050.04390.207-0.137-0.1599-0.09790.18870.0214-0.14260.08190.1591-0.00770.01260.1384-0.04840.15311.92166.786749.1598
53.1927-0.26110.69433.9756-0.78664.11810.12390.19-0.2128-0.05280.02530.14590.1692-0.0437-0.11790.16570.0120.03490.1186-0.01530.136222.97093.038854.1175
62.3089-0.4342-0.81452.89021.48722.0298-0.055-0.3553-0.02120.36460.0872-0.32520.14860.2830.06690.22340.0194-0.03330.22270.02110.195929.540312.530867.0094
72.63430.13470.19853.39810.06794.05410.19120.2611-0.0383-0.1772-0.2416-0.13870.23650.48160.05630.19820.07220.0150.2949-0.02610.258546.972815.14938.8281
81.9964-1.07990.76512.09950.03382.08050.59110.4126-0.5706-0.7134-0.23070.3790.81920.4577-0.2790.50310.1432-0.14580.3311-0.08810.421936.942312.744824.8145
91.9044-2.28272.2364.2696-2.46133.81560.21610.1249-0.2588-0.542-0.07880.37080.0936-0.0202-0.10820.28610.0514-0.02080.2530.03580.288122.823133.179721.4512
102.6332-1.42290.9863.3485-0.91583.24220.00830.08210.18980.0773-0.0606-0.0862-0.31990.06250.04670.1943-0.02180.02030.20140.04080.17537.988529.675140.9234
113.25370.01931.10554.32110.65075.5219-0.0434-0.5418-0.05130.1847-0.00470.4667-0.2156-0.28510.04350.20420.00980.04630.28680.00170.23480.288716.55594.9317
121.8284-0.5481-0.07461.7269-0.20611.2052-0.0301-0.13660.2010.0441-0.0133-0.1343-0.0720.10190.04390.1623-0.0297-0.01970.198-0.03330.17589.872325.773-4.0806
132.8085-0.28261.33152.46650.05254.1774-0.08930.16640.0639-0.1141-0.0156-0.1819-0.2060.34430.07330.1864-0.0192-0.00780.16840.0330.206921.960970.820622.2726
143.53080.26840.22942.2388-0.2592.3198-0.2013-0.09250.44420.20880.0418-0.1175-0.6326-0.06330.11660.33880.0296-0.08770.1963-0.04190.253916.851577.732232.158
152.7080.58850.46982.57890.13612.784-0.0891-0.577-0.04370.47390.05340.2893-0.0194-0.30320.02130.2510.06430.04540.40120.02130.20292.182963.769139.5286
164.9836-0.4408-0.71283.28990.87083.8789-0.0691-0.3145-0.19050.1360.06150.5265-0.0328-0.3726-0.00450.1816-0.00850.01920.24730.0710.24481.58154.138226.4968
171.74390.61740.48484.5589-0.20111.83280.03690.0915-0.1216-0.0839-0.0012-0.25270.13650.1452-0.03180.19470.03310.01490.21890.01930.175719.890356.868319.8077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 18 through 43 )
2X-RAY DIFFRACTION2chain 'D' and (resid 44 through 127 )
3X-RAY DIFFRACTION3chain 'D' and (resid 128 through 191 )
4X-RAY DIFFRACTION4chain 'D' and (resid 192 through 233 )
5X-RAY DIFFRACTION5chain 'D' and (resid 234 through 304 )
6X-RAY DIFFRACTION6chain 'D' and (resid 305 through 344 )
7X-RAY DIFFRACTION7chain 'A' and (resid 15 through 43 )
8X-RAY DIFFRACTION8chain 'A' and (resid 44 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 211 )
10X-RAY DIFFRACTION10chain 'A' and (resid 212 through 343 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 343 )
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 43 )
14X-RAY DIFFRACTION14chain 'C' and (resid 44 through 105 )
15X-RAY DIFFRACTION15chain 'C' and (resid 106 through 211 )
16X-RAY DIFFRACTION16chain 'C' and (resid 212 through 264 )
17X-RAY DIFFRACTION17chain 'C' and (resid 265 through 343 )

+
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://pdbjlvh1.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