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- PDB-5yps: The structural basis of histone chaperoneVps75 -

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Basic information

Entry
Database: PDB / ID: 5yps
TitleThe structural basis of histone chaperoneVps75
ComponentsVacuolar protein sorting-associated protein 75
KeywordsCHAPERONE / Histone chaperone / acetylation
Function / homology
Function and homology information


: / nucleosome assembly / histone binding / nucleus
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Similarity search - Component
Biological speciesPneumocystis carinii B80 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.097 Å
AuthorsChen, Y. / Zhang, Y. / Dou, Y. / Wang, M. / Xu, S. / Jiang, H. / Limper, A. / Su, D.
Funding support China, 4items
OrganizationGrant numberCountry
National Key Research and Development Program of China2017YFA0505900 China
The General Program of National Natural Science Foundation of China31370735 China
The General Program of National Natural Science Foundation of China3167040397 China
The Province Science and Technology Support Program,2015JQO029 China
CitationJournal: Signal Transduct Target Ther / Year: 2019
Title: Structural basis for the acetylation of histone H3K9 and H3K27 mediated by the histone chaperone Vps75 inPneumocystis carinii.
Authors: Chen, Y. / Zhang, Y. / Ye, H. / Dou, Y. / Lu, D. / Li, X. / Limper, A.H. / Hua, J. / Su, D.
History
DepositionNov 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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
Revision 1.2Jun 10, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75
C: Vacuolar protein sorting-associated protein 75
D: Vacuolar protein sorting-associated protein 75
E: Vacuolar protein sorting-associated protein 75
F: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,18257
Polymers176,1906
Non-polymers6,99251
Water4,179232
1
A: Vacuolar protein sorting-associated protein 75
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,84918
Polymers58,7302
Non-polymers2,11916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-54 kcal/mol
Surface area21170 Å2
MethodPISA
2
C: Vacuolar protein sorting-associated protein 75
D: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,90517
Polymers58,7302
Non-polymers2,17515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-52 kcal/mol
Surface area20950 Å2
MethodPISA
3
E: Vacuolar protein sorting-associated protein 75
F: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,42922
Polymers58,7302
Non-polymers2,69920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-55 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.672, 76.404, 130.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Vacuolar protein sorting-associated protein 75


Mass: 29365.027 Da / Num. of mol.: 6 / Mutation: N56M, E127M, G194E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pneumocystis carinii B80 (fungus) / Strain: B80 / Gene: T552_02523 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W4ZF97

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Non-polymers , 6 types, 283 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Calcium chloride dihydrate, HEPES sodium, PEG 400

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Apr 5, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.09→48.26 Å / Num. obs: 83282 / % possible obs: 100 % / Redundancy: 7 % / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.097→48.26 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.94
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 4088 4.91 %0.05
Rwork0.1857 ---
obs0.1881 83282 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.097→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9807 0 446 232 10485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810536
X-RAY DIFFRACTIONf_angle_d1.08514160
X-RAY DIFFRACTIONf_dihedral_angle_d19.6383975
X-RAY DIFFRACTIONf_chiral_restr0.0441507
X-RAY DIFFRACTIONf_plane_restr0.0051802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0972-2.12190.26961060.24782439X-RAY DIFFRACTION88
2.1219-2.14780.31821420.2322662X-RAY DIFFRACTION100
2.1478-2.17490.3561220.22922749X-RAY DIFFRACTION100
2.1749-2.20360.29021540.21532683X-RAY DIFFRACTION100
2.2036-2.23370.28071330.21252713X-RAY DIFFRACTION100
2.2337-2.26570.28261470.21182703X-RAY DIFFRACTION100
2.2657-2.29950.24271440.20012704X-RAY DIFFRACTION100
2.2995-2.33540.26171360.19682721X-RAY DIFFRACTION100
2.3354-2.37370.25931460.20242718X-RAY DIFFRACTION100
2.3737-2.41460.29391350.20942713X-RAY DIFFRACTION100
2.4146-2.45850.28081410.20722708X-RAY DIFFRACTION100
2.4585-2.50580.23831310.19972711X-RAY DIFFRACTION100
2.5058-2.5570.28221800.19652730X-RAY DIFFRACTION100
2.557-2.61260.25061690.19612672X-RAY DIFFRACTION100
2.6126-2.67330.23841490.19452716X-RAY DIFFRACTION100
2.6733-2.74020.24931550.21392709X-RAY DIFFRACTION100
2.7402-2.81420.28381520.21582698X-RAY DIFFRACTION100
2.8142-2.89710.3151570.21612726X-RAY DIFFRACTION100
2.8971-2.99050.28221690.22812706X-RAY DIFFRACTION100
2.9905-3.09740.27521320.21172757X-RAY DIFFRACTION100
3.0974-3.22140.25381240.20442766X-RAY DIFFRACTION100
3.2214-3.3680.22561380.19652740X-RAY DIFFRACTION100
3.368-3.54550.23331320.17462757X-RAY DIFFRACTION100
3.5455-3.76760.20191260.16042775X-RAY DIFFRACTION100
3.7676-4.05830.18471150.15352811X-RAY DIFFRACTION100
4.0583-4.46650.18551110.14182819X-RAY DIFFRACTION100
4.4665-5.11210.18521400.15232793X-RAY DIFFRACTION100
5.1121-6.43830.22111510.18722843X-RAY DIFFRACTION100
6.4383-48.27280.22391510.19222952X-RAY DIFFRACTION100
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)
11.0636-0.04620.21862.12370.0721.7183-0.01470.2183-0.0345-0.0714-0.0051-0.1529-0.12780.19310.01380.2229-0.0359-0.01910.28840.00870.2536-16.212316.4802-56.3865
21.5204-0.0470.44681.72750.26272.3714-0.0591-0.1480.03830.06820.01270.1029-0.2905-0.20630.0470.34150.0011-0.04140.232-0.01270.2555-28.835629.2767-33.284
32.2018-0.01880.02291.4621-0.26822.4201-0.0870.0424-0.04970.13970.0095-0.00120.0951-0.09960.07210.2808-0.00490.02320.19530.0160.2473-34.2935-0.477-30.9316
41.47910.13950.22491.6874-0.03092.63-0.12760.11720.0333-0.07490.1160.0881-0.0069-0.47120.02050.2691-0.0193-0.02920.4299-0.02630.253-45.69349.1866-56.4905
51.89280.16550.00641.3585-0.08862.01050.0338-0.04950.0439-0.0514-0.01350.0708-0.0031-0.2786-0.02010.1980.0223-0.02210.2303-0.01160.1951-15.015840.8102-9.0024
61.7863-0.2525-0.16181.45540.03931.8674-0.0368-0.2224-0.12980.09530.0558-0.02060.2509-0.1717-0.02510.2876-0.00520.03130.30270.02920.2642-8.079825.332815.0366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 19:220)
2X-RAY DIFFRACTION2(chain B and resseq 20:219)
3X-RAY DIFFRACTION3(chain C and resseq 20:220)
4X-RAY DIFFRACTION4(chain D and resseq 20:219)
5X-RAY DIFFRACTION5(chain E and resseq 20:221)
6X-RAY DIFFRACTION6(chain F and resseq 20:220)

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