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- PDB-5l0y: Crystal Structure of a Sec72-ssa1 c-terminal peptide fusion protein -

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Basic information

Entry
Database: PDB / ID: 5l0y
TitleCrystal Structure of a Sec72-ssa1 c-terminal peptide fusion protein
Components
  • PRO-THR-VAL-GLU-GLU-VAL-ASP
  • Sec72-ssa1 c-terminal peptide fusion protein
KeywordsPROTEIN TRANSPORT / Protein translocation / TPR / C-terminal Ssa1 peptide / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


Hsp70 protein binding / Hsp90 protein binding / ATP-dependent protein folding chaperone / protein folding / ATP binding / nucleus / cytosol
Similarity search - Function
Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Tetratricopeptide repeats / Tetratricopeptide repeat ...Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / Tetratricopeptide repeats / Tetratricopeptide repeat / ATPase, nucleotide binding domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Heat shock protein 70-like protein / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsTripathi, A. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Two alternative binding mechanisms connect the protein translocation Sec71-Sec72 complex with heat shock proteins.
Authors: Tripathi, A. / Mandon, E.C. / Gilmore, R. / Rapoport, T.A.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3May 29, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sec72-ssa1 c-terminal peptide fusion protein
B: Sec72-ssa1 c-terminal peptide fusion protein
C: Sec72-ssa1 c-terminal peptide fusion protein
D: Sec72-ssa1 c-terminal peptide fusion protein
E: Sec72-ssa1 c-terminal peptide fusion protein
F: Sec72-ssa1 c-terminal peptide fusion protein
G: Sec72-ssa1 c-terminal peptide fusion protein
H: Sec72-ssa1 c-terminal peptide fusion protein
I: PRO-THR-VAL-GLU-GLU-VAL-ASP
J: PRO-THR-VAL-GLU-GLU-VAL-ASP
K: PRO-THR-VAL-GLU-GLU-VAL-ASP
L: PRO-THR-VAL-GLU-GLU-VAL-ASP
M: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)149,47813
Polymers149,47813
Non-polymers00
Water00
1
A: Sec72-ssa1 c-terminal peptide fusion protein
D: Sec72-ssa1 c-terminal peptide fusion protein


Theoretical massNumber of molelcules
Total (without water)36,3852
Polymers36,3852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sec72-ssa1 c-terminal peptide fusion protein
M: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sec72-ssa1 c-terminal peptide fusion protein
I: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sec72-ssa1 c-terminal peptide fusion protein
L: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sec72-ssa1 c-terminal peptide fusion protein
H: Sec72-ssa1 c-terminal peptide fusion protein


Theoretical massNumber of molelcules
Total (without water)36,3852
Polymers36,3852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Sec72-ssa1 c-terminal peptide fusion protein
J: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Sec72-ssa1 c-terminal peptide fusion protein
K: PRO-THR-VAL-GLU-GLU-VAL-ASP


Theoretical massNumber of molelcules
Total (without water)18,9802
Polymers18,9802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.504, 118.535, 164.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Sec72-ssa1 c-terminal peptide fusion protein


Mass: 18192.420 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Saccharomyces cerevisiae S288c (yeast)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0068610 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SH41
#2: Protein/peptide
PRO-THR-VAL-GLU-GLU-VAL-ASP


Mass: 787.811 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYP6*PLUS

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ammonium citrate pH 7.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.87→164.05 Å / Num. obs: 34691 / % possible obs: 99.3 % / Redundancy: 2 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L0W

5l0w


Resolution: 2.87→96.08 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1747 5.04 %
Rwork0.236 --
obs0.238 34678 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.98 Å2
Refinement stepCycle: LAST / Resolution: 2.87→96.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9720 0 0 0 9720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079866
X-RAY DIFFRACTIONf_angle_d1.0613229
X-RAY DIFFRACTIONf_dihedral_angle_d19.9173847
X-RAY DIFFRACTIONf_chiral_restr0.0481354
X-RAY DIFFRACTIONf_plane_restr0.0041751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.95450.38551430.32292718X-RAY DIFFRACTION100
2.9545-3.04980.4091980.34332751X-RAY DIFFRACTION100
3.0498-3.15880.41131470.33782683X-RAY DIFFRACTION99
3.1588-3.28530.36581470.28552723X-RAY DIFFRACTION99
3.2853-3.43490.32091510.26492708X-RAY DIFFRACTION99
3.4349-3.61590.35681230.26162735X-RAY DIFFRACTION99
3.6159-3.84250.28881530.23252712X-RAY DIFFRACTION99
3.8425-4.13920.26231630.22052714X-RAY DIFFRACTION100
4.1392-4.55570.26171540.20092756X-RAY DIFFRACTION100
4.5557-5.21490.28141570.21942750X-RAY DIFFRACTION99
5.2149-6.570.27461690.23372777X-RAY DIFFRACTION99
6.57-96.13240.19571420.19682904X-RAY DIFFRACTION98

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