[English] 日本語
Yorodumi
- PDB-7ef3: crystal structure of maize SHH2 SAWADEE domain in complex with H3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ef3
Titlecrystal structure of maize SHH2 SAWADEE domain in complex with H3K9me2 peptide
Components
  • HB transcription factor
  • Histone H3.2
KeywordsGENE REGULATION / SHH2 / maize / H3K9me2 / histone
Function / homology
Function and homology information


chromocenter / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / metal ion binding / nucleus
Similarity search - Function
SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / Homeobox-like domain superfamily / SH3 type barrels. ...SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SH3 type barrels. - #140 / Homeobox-like domain superfamily / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HB transcription factor / Histone H3.2
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, Y. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770782 China
CitationJournal: J Integr Plant Biol / Year: 2021
Title: Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.
Authors: Wang, Y. / Zhou, X. / Luo, J. / Lv, S. / Liu, R. / Du, X. / Jia, B. / Yuan, F. / Zhang, H. / Du, J.
History
DepositionMar 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: HB transcription factor
B: HB transcription factor
P: Histone H3.2
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3146
Polymers38,1834
Non-polymers1312
Water1,802100
1
A: HB transcription factor
P: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1573
Polymers19,0922
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-2 kcal/mol
Surface area9370 Å2
MethodPISA
2
B: HB transcription factor
Q: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1573
Polymers19,0922
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.906, 67.370, 80.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HB transcription factor / Protein SAWADEE HOMEODOMAIN HOMOLOG 2


Mass: 17914.150 Da / Num. of mol.: 2 / Mutation: R235G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100279552, HB131, ZEAMMB73_Zm00001d005584 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7ZYP9
#2: Protein/peptide Histone H3.2


Mass: 1177.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize) / References: UniProt: P69246
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH7.5, 70% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2015
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21207 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Χ2: 1 / Net I/σ(I): 5.1 / Num. measured all: 111652
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.184.90.7620900.7410.3740.850.48899.5
2.18-2.265.20.58620600.8460.2810.6520.52999.9
2.26-2.375.30.48920810.8910.2320.5430.549100
2.37-2.495.10.40321090.9090.1970.450.60799.9
2.49-2.655.40.29420790.9470.1390.3260.67899.6
2.65-2.855.60.22721130.970.1060.2510.781100
2.85-3.145.40.14621200.9850.0690.1621.0699.9
3.14-3.595.30.10321290.9890.0490.1141.56699.8
3.59-4.525.40.07621700.9920.0370.0851.908100
4.52-5050.06222560.9940.030.0691.7198.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EEZ

7eez


Resolution: 2.1→34.13 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1083 5.14 %
Rwork0.2188 19982 -
obs0.2213 21065 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.31 Å2 / Biso mean: 47.0014 Å2 / Biso min: 22.34 Å2
Refinement stepCycle: final / Resolution: 2.1→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 2 100 2596
Biso mean--40.68 49.99 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022548
X-RAY DIFFRACTIONf_angle_d0.6393432
X-RAY DIFFRACTIONf_chiral_restr0.026360
X-RAY DIFFRACTIONf_plane_restr0.003456
X-RAY DIFFRACTIONf_dihedral_angle_d13.844960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.19560.30511430.2716242599
2.1956-2.31130.26371420.25152454100
2.3113-2.45610.29191400.24922467100
2.4561-2.64570.36771240.25262462100
2.6457-2.91180.2851370.23182500100
2.9118-3.33280.25791340.21152513100
3.3328-4.19780.22511490.18832507100
4.1978-34.130.27561140.2174265499
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)
14.37154.6413-2.22235.0173-2.80526.6849-0.07570.0269-0.11030.27990.36540.0419-0.3593-1.1544-0.23610.4079-0.0038-0.02030.3945-0.01850.4153-21.194810.5487-14.3705
24.76250.39971.30892.55461.9885.1561-0.2631-0.26630.8305-0.445-0.08620.1078-0.29770.07230.06160.38860.0113-0.04470.28610.04950.4506-15.125720.251-17.541
37.1786-0.5413-0.11085.06391.48096.873-0.90981.17450.5149-0.01130.9108-0.6885-0.03490.7614-0.14240.6109-0.10990.00950.5844-0.07470.3567-12.375911.2256-31.9088
49.0522-2.1085-0.20188.44571.14164.22680.62580.09061.5028-0.9285-0.2901-0.3985-1.24220.12920.01450.6305-0.0240.03740.3640.03220.4023-19.779322.6917-23.3817
55.2987-0.72691.00165.1237-1.49189.6629-0.27470.1509-0.2814-0.17130.0689-0.09440.118-0.3120.15530.1897-0.0546-0.03640.1935-0.01420.31-15.201913.1367-15.7537
64.6134-1.57260.17484.3685-1.054.2324-0.2472-0.36210.04910.31270.1102-0.1658-0.50630.1044-0.12560.30.0318-0.04290.2666-0.09330.3321-10.509618.253-1.4832
74.7824-1.49040.20264.26620.32093.4347-1.4823-1.45671.08692.13170.71940.65250.2974-0.7775-0.11840.82440.20510.12570.6928-0.08740.5228-17.59317.58313.4893
85.35383.4596-0.37257.3664-4.8454.0863-0.10120.06630.37220.19460.1065-0.44720.03290.0209-0.10940.3280.0345-0.00090.263-0.03390.4199-4.035519.9902-1.7447
91.2364-0.76641.60584.21360.95035.0318-0.18760.03690.34720.17610.38-0.2405-0.40480.5410.15590.26460.00910.06640.4249-0.05880.3565-12.375418.73030.376
106.24730.599-1.30445.7563-1.43038.4328-0.5-0.553-0.62610.6513-0.12430.66810.8296-0.44810.23040.4692-0.03840.09670.43030.04930.5744-19.82190.4252.8686
116.60424.07291.98045.26110.74096.33490.07390.9938-1.3440.18080.3080.08140.6726-0.491-0.26290.5401-0.03930.09210.5093-0.01360.5061-8.8594-8.61254.9873
125.532.3559-2.42233.6928-1.93467.60630.1794-0.53510.22850.3163-0.4102-0.0991-0.60571.289-0.42460.4775-0.0538-0.05850.50320.08380.4097-0.6833-4.438115.0012
133.6742-0.11710.86045.74130.59737.64180.1474-0.2998-0.0833-0.3185-0.2485-1.39140.30632.05520.11270.56010.04680.03370.70050.11590.65642.888-12.545914.0062
142.7756-0.3474-0.11932.94-2.69836.6494-0.13010.1239-0.31360.0071-0.0356-0.21260.24710.27860.01610.2592-0.0070.0410.31630.00060.3692-2.8942-2.7439-0.9336
157.72861.21141.75851.3884-2.00784.73921.5346-0.045-0.5729-0.2457-0.112-1.84560.96981.6867-0.22830.48450.13290.19061.16450.07121.404615.5623-7.2123-2.9458
164.1059-0.69710.62564.50231.0147.2249-0.01140.5557-0.0612-0.8083-0.0367-0.0318-0.56760.49210.23080.4485-0.02910.00740.3061-0.08790.41363.34821.9522-6.9929
171.8818-2.2772-0.42788.88692.73266.933-0.01190.01940.0339-0.6968-0.14810.57490.1629-0.19580.31010.5413-0.03520.01660.5654-0.1020.4855-0.4677-5.8191-22.9895
186.20821.14773.83553.7054-0.65753.25730.20290.3125-0.30040.11510.2597-0.14040.21110.6204-0.31040.396-0.0280.05510.341-0.07630.37756.81314.4686-6.7173
197.14311.0092-2.43214.3289-0.13497.0188-0.12330.1794-0.3666-0.49230.1467-0.71640.31740.34010.29670.41380.00570.11740.4552-0.09990.43652.5238-2.7295-9.6332
206.2884-1.66452.09395.93940.49448.67430.09840.8689-1.3309-0.9973-0.28941.31080.675-1.5502-0.17630.5015-0.0373-0.03820.6466-0.12170.7667-16.8049-2.9102-11.6644
214.3622-1.9325-0.72887.6965-1.69342.93690.1924-1.06070.15270.15390.24430.3179-0.6022-0.1367-0.83550.4755-0.10210.01530.4503-0.03840.5804-20.730322.8514-6.616
227.06294.2415-4.46975.8398-2.81052.80891.1412-0.8357-1.6636-0.2234-0.8199-0.9389-0.66740.80791.29351.42070.34790.00561.01510.05450.839410.0901-11.98480.7818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 131 through 139 )A131 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 152 )A140 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 163 )A153 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 177 )A164 - 177
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 194 )A178 - 194
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 228 )A195 - 228
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 239 )A229 - 239
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 250 )A240 - 250
9X-RAY DIFFRACTION9chain 'A' and (resid 251 through 262 )A251 - 262
10X-RAY DIFFRACTION10chain 'A' and (resid 263 through 278 )A263 - 278
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 139 )B131 - 139
12X-RAY DIFFRACTION12chain 'B' and (resid 140 through 163 )B140 - 163
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 177 )B164 - 177
14X-RAY DIFFRACTION14chain 'B' and (resid 178 through 211 )B178 - 211
15X-RAY DIFFRACTION15chain 'B' and (resid 212 through 217 )B212 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 228 )B218 - 228
17X-RAY DIFFRACTION17chain 'B' and (resid 229 through 239 )B229 - 239
18X-RAY DIFFRACTION18chain 'B' and (resid 240 through 250 )B240 - 250
19X-RAY DIFFRACTION19chain 'B' and (resid 251 through 262 )B251 - 262
20X-RAY DIFFRACTION20chain 'B' and (resid 263 through 277 )B263 - 277
21X-RAY DIFFRACTION21chain 'P' and (resid 2 through 8 )P2 - 8
22X-RAY DIFFRACTION22chain 'Q' and (resid 5 through 9 )Q5 - 9

+
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