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- PDB-7ybf: Crystal structure of inner membrane protein Sad1 in complex with ... -

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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 / mating-type region heterochromatin / meiotic spindle pole / meiotic nuclear membrane microtubule tethering complex / 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 / nuclear envelope / heterochromatin formation / nucleosome / 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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