[English] 日本語
Yorodumi
- PDB-7ybf: Crystal structure of inner membrane protein Sad1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ybf
TitleCrystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B
Components
  • Histone H2B-alpha,Histone H2A-beta
  • Spindle pole body-associated protein sad1
KeywordsMEMBRANE PROTEIN / Heterochromatin / Histone chaperone / Histone / Phase separation
Function / homology
Function and homology information


old mitotic spindle pole body / spindle pole body-nuclear membrane anchor activity / mitotic spindle pole body insertion into the nuclear envelope / Sad1-Kms1 LINC complex / inner plaque of mitotic spindle pole body / centromere clustering at the mitotic interphase nuclear envelope / Condensation of Prophase Chromosomes / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...old mitotic spindle pole body / spindle pole body-nuclear membrane anchor activity / mitotic spindle pole body insertion into the nuclear envelope / Sad1-Kms1 LINC complex / inner plaque of mitotic spindle pole body / centromere clustering at the mitotic interphase nuclear envelope / Condensation of Prophase Chromosomes / HATs acetylate histones / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / meiotic attachment of telomeric heterochromatin to spindle pole body / new mitotic spindle pole body / Oxidative Stress Induced Senescence / meiotic spindle pole body / RMTs methylate histone arginines / Ub-specific processing proteases / HDACs deacetylate histones / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transcriptional regulation by small RNAs / meiotic nuclear membrane microtubule tethering complex / mating-type region heterochromatin / meiotic spindle pole / mitotic DNA damage checkpoint signaling / chromosome, subtelomeric region / mitotic spindle pole body / homologous chromosome segregation / interphase microtubule organizing center / rDNA heterochromatin / chromatin-protein adaptor activity / mitotic chromosome condensation / nuclear inner membrane / mitotic G2 DNA damage checkpoint signaling / pericentric heterochromatin / protein-membrane adaptor activity / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / nuclear envelope / heterochromatin formation / double-strand break repair / site of double-strand break / protein-macromolecule adaptor activity / microtubule / chromatin remodeling / protein heterodimerization activity / cell division / DNA binding / nucleus / cytoplasm
Similarity search - Function
SUN domain-containing protein 1-5 / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain ...SUN domain-containing protein 1-5 / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A-beta / Histone H2B-alpha / Spindle pole body-associated protein sad1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSun, W. / Hu, C. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010303 China
CitationJournal: Nat Commun / Year: 2024
Title: The SUN-family protein Sad1 mediates heterochromatin spatial organization through interaction with histone H2A-H2B.
Authors: Sun, W. / Dong, Q. / Li, X. / Gao, J. / Ye, X. / Hu, C. / Li, F. / Chen, Y.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H2B-alpha,Histone H2A-beta
B: Histone H2B-alpha,Histone H2A-beta
C: Spindle pole body-associated protein sad1


Theoretical massNumber of molelcules
Total (without water)43,4423
Polymers43,4423
Non-polymers00
Water1,74797
1
A: Histone H2B-alpha,Histone H2A-beta
C: Spindle pole body-associated protein sad1


Theoretical massNumber of molelcules
Total (without water)22,7252
Polymers22,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone H2B-alpha,Histone H2A-beta


Theoretical massNumber of molelcules
Total (without water)20,7181
Polymers20,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.804, 61.981, 76.016
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Histone H2B-alpha,Histone H2A-beta / H2B.1 / H2A.2


Mass: 20717.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: htb1, SPCC622.09, hta2, SPAC19G12.06c / Production host: Escherichia coli (E. coli) / References: UniProt: P04913, UniProt: P04910
#2: Protein/peptide Spindle pole body-associated protein sad1


Mass: 2006.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: sad1, SPBC12D12.01, SPBC16H5.01c / Production host: Escherichia coli (E. coli) / References: UniProt: Q09825
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium nitrate, 20% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 21380 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.057 / Rrim(I) all: 0.136 / Χ2: 0.915 / Net I/σ(I): 5.6 / Num. measured all: 118345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.235.50.55221140.7890.2560.610.84999.7
2.23-2.325.20.45120950.8560.2150.5011.05899.7
2.32-2.425.70.34921330.9130.1590.3840.95399.8
2.42-2.555.70.27421330.940.1240.3010.99299.9
2.55-2.715.60.23221450.9510.1070.2570.99599.9
2.71-2.925.40.18121140.9680.0850.2011.01899.8
2.92-3.215.80.15121260.9740.0680.1660.98999.8
3.21-3.685.50.10921610.9830.0510.120.891100
3.68-4.635.70.08721580.990.040.0960.725100
4.63-505.40.08622010.9910.0410.0960.68999.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNN

4wnn


Resolution: 2.15→37.19 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 1983 9.43 %
Rwork0.198 19053 -
obs0.2028 21036 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.32 Å2 / Biso mean: 29.6401 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: final / Resolution: 2.15→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 0 97 2946
Biso mean---35.76 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.2911330.21891294142795
2.2-2.260.25711370.21061307144495
2.26-2.330.29341340.21191311144597
2.33-2.410.2421470.2011363151099
2.41-2.490.27781380.203813631501100
2.49-2.590.25041470.201113721519100
2.59-2.710.27121260.20631384151099
2.71-2.850.26161480.20381371151999
2.85-3.030.24871360.206613731509100
3.03-3.260.26321470.208813781525100
3.26-3.590.21331410.196913901531100
3.59-4.110.23381490.175513611510100
4.11-5.180.22261480.18561378152699
5.18-37.190.26171520.20071408156099
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)
10.6306-0.00720.50620.4916-0.3030.44370.03520.13710.14120.0110.0492-0.1629-0.07550.1729-0.00010.12290.01370.01380.18360.01970.20744.1392-11.8484-46.5998
20.4697-0.29140.38160.5106-0.17590.4791-0.1942-0.32480.26030.1921-0.054-0.0459-0.5387-0.4316-0.02580.21760.0086-0.00590.19310.00790.15572.4753-12.5701-29.4629
30.113-0.0062-0.23110.3396-0.14510.2938-0.0822-0.14330.12070.1967-0.0057-0.10460.16790.2571-0.01290.25120.0118-0.02420.20290.01830.140313.4947-18.2316-22.6049
41.40840.7625-0.09921.0765-0.54581.30570.0994-0.1119-0.02020.1886-0.2227-0.33170.16070.2394-0.04070.1542-0.0157-0.00210.18990.02710.217917.2244-12.2687-34.1061
50.2340.02370.29670.3074-0.48630.23520.10320.1110.0613-0.02380.00660.01240.11860.10930.00010.1486-0.00720.00840.1510.00760.14856.3516-19.3427-40.5241
60.2797-0.05840.15040.15220.06780.22760.0841-0.1194-0.10630.14780.31590.3640.3431-0.81960.01470.2368-0.0461-0.01480.25240.04210.1982-8.0657-21.1844-47.2963
70.85321.7018-0.75374.8264-1.22010.8640.45170.15620.2358-0.03850.3271.0940.0602-0.55420.26720.4224-0.0764-0.01490.2224-0.05170.1214-3.9207-25.1631-32.9409
81.1449-0.1711-0.34410.4822-0.33720.2908-0.0867-0.5132-0.17680.1610.1611-0.43340.45650.2685-0.0120.12280.00620.03010.24040.01970.2247-7.4715-29.76587.9151
90.9879-0.48650.172.04060.17340.9067-0.15730.5472-0.9124-0.9211-0.45470.76260.3293-0.3797-0.22650.1136-0.0842-0.13640.0839-0.0770.032-2.0362-29.3748-8.5683
100.83550.1888-0.13840.4521-0.89190.68640.11250.12910.0938-0.0091-0.1659-0.1126-0.17190.27790.00030.22210.0322-0.00360.1848-0.00950.145610.0394-22.6391-4.5982
110.60940.33020.22180.8481-0.2460.29580.0878-0.0183-0.72870.12450.081-0.14180.44360.20080.05680.22570.0638-0.03490.2401-0.05520.38459.1134-36.1843-0.3775
120.5846-0.08110.36110.90010.0020.67450.1024-0.21010.0622-0.05510.0809-0.03890.04390.00740.00240.13490.007-0.00490.14650.03180.1767-6.7583-22.44354.5949
130.1243-0.2401-0.04640.1728-0.27310.29770.27470.51090.4466-0.2332-0.15380.4758-0.3853-0.63860.00330.28680.03820.00040.29920.06250.2898-12.6368-17.4893-4.0185
140.0993-0.10980.00010.28550.14980.36210.5067-0.06860.3538-0.6403-0.3060.1116-0.20530.2250.00860.52-0.07150.0160.38360.05080.3276-2.1001-4.8513-50.3037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 58 )A37 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 87 )A59 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 106 )A88 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 161 )A107 - 161
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 189 )A162 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 206 )A190 - 206
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 216 )A207 - 216
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 58 )B37 - 58
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 87 )B59 - 87
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 126 )B88 - 126
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 161 )B127 - 161
12X-RAY DIFFRACTION12chain 'B' and (resid 162 through 196 )B162 - 196
13X-RAY DIFFRACTION13chain 'B' and (resid 197 through 215 )B197 - 215
14X-RAY DIFFRACTION14chain 'C' and (resid 112 through 123 )C112 - 123

+
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