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- PDB-3mp7: Lateral opening of a translocon upon entry of protein suggests th... -

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Basic information

Entry
Database: PDB / ID: 3mp7
TitleLateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes
Components
  • Preprotein translocase subunit secE
  • Preprotein translocase subunit secY
KeywordsPROTEIN TRANSPORT / Membrane Protein Complex / Preprotein Translocase / Membrane Insertion / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


intracellular protein transmembrane transport / protein transmembrane transporter activity / protein secretion / protein targeting / plasma membrane
Similarity search - Function
Preprotein translocase SecE subunit / Preprotein translocase SecY subunit / SecY subunit domain / Protein translocase subunit SecY / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. ...Preprotein translocase SecE subunit / Preprotein translocase SecY subunit / SecY subunit domain / Protein translocase subunit SecY / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsEgea, P.F. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes.
Authors: Egea, P.F. / Stroud, R.M.
History
DepositionApr 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Preprotein translocase subunit secY
B: Preprotein translocase subunit secE


Theoretical massNumber of molelcules
Total (without water)60,8842
Polymers60,8842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-34 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.240, 141.570, 235.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Preprotein translocase subunit secY / Protein transport protein SEC61 subunit alpha homolog


Mass: 53939.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: secY / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q8U019
#2: Protein Preprotein translocase subunit secE / Protein transport protein Sec61 gamma subunit homolog


Mass: 6944.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: secE / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: Q8TZK2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.4 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG4000-PEG8000 15-25%, MES 100mM pH 6.2, Ca or Mg Acetate 50-200mM, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.97966, 0.97958, 0.96863
SYNCHROTRONALS 8.3.121.115872
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979661
20.979581
30.968631
41.1158721
ReflectionResolution: 2.9→50 Å / Num. obs: 23475 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 90.3 Å2 / Rsym value: 0.672 / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassification
ELVESrefinement
PHENIXmodel building
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1RH5

1rh5


Resolution: 2.9→49.43 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.793 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1375 8.29 %RANDOM
Rwork0.277 ---
obs0.28 16582 --
Displacement parametersBiso max: 176.69 Å2 / Biso mean: 78.672 Å2 / Biso min: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.682 Å20 Å20 Å2
2---3.136 Å20 Å2
3---3.819 Å2
Refine analyzeLuzzati coordinate error obs: 0.615 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 0 3362
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0134792
X-RAY DIFFRACTIONt_angle_deg1.347402
X-RAY DIFFRACTIONt_dihedral_angle_d11242
X-RAY DIFFRACTIONt_trig_c_planes422
X-RAY DIFFRACTIONt_gen_planes5155
X-RAY DIFFRACTIONt_it347920
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion24.02
X-RAY DIFFRACTIONt_chiral_improper_torsion4805
X-RAY DIFFRACTIONt_ideal_dist_contact41754
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.312 34 10.62 %
Rwork0.281 286 -
all0.284 320 -

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