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- PDB-2yxq: The plug domain of the SecY protein stablizes the closed state of... -

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Basic information

Entry
Database: PDB / ID: 2yxq
TitleThe plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal
Components
  • Preprotein translocase secG subunit
  • Preprotein translocase subunit secE
  • Preprotein translocase subunit secY
KeywordsPROTEIN TRANSPORT / protein translocation / signal peptide / membrane protein / protein secretion / prl mutation
Function / homology
Function and homology information


intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein secretion / protein transmembrane transporter activity / protein targeting / protein transport / plasma membrane
Similarity search - Function
Preprotein translocase SecE subunit / Preprotein translocase SecY subunit / SecY subunit domain / Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain ...Preprotein translocase SecE subunit / Preprotein translocase SecY subunit / SecY subunit domain / Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / 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. / SecE/Sec61-gamma subunits of protein translocation complex / 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
Preprotein translocase subunit SecG / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLi, W. / Schulman, S.
CitationJournal: Mol.Cell / Year: 2007
Title: The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal
Authors: Li, W. / Schulman, S. / Boyd, D. / Erlandson, K. / Beckwith, J. / Rapoport, T.A.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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
Remark 999SEQUENCE deletion of 60-65 and substitution with one Gly

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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
C: Preprotein translocase secG subunit


Theoretical massNumber of molelcules
Total (without water)61,3563
Polymers61,3563
Non-polymers00
Water00
1
A: Preprotein translocase subunit secY


Theoretical massNumber of molelcules
Total (without water)46,9381
Polymers46,9381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Preprotein translocase subunit secE


Theoretical massNumber of molelcules
Total (without water)8,4511
Polymers8,4511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Preprotein translocase secG subunit


Theoretical massNumber of molelcules
Total (without water)5,9671
Polymers5,9671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-64 kcal/mol
Surface area27920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.235, 148.489, 81.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer in the asymmetric unit

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Components

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


Mass: 46938.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: secY / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q60175
#2: Protein Preprotein translocase subunit secE / Protein transport protein SEC61 gamma subunit homolog


Mass: 8451.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: secE / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q57817
#3: Protein Preprotein translocase secG subunit / Protein transport protein SEC61 subunit beta homolog


Mass: 5967.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: secG / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P60460

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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: 4.82 Å3/Da / Density % sol: 74.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40-55% PEG400, 50mM Glycine-HCl , pH9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 14806 / Num. obs: 14678 / % possible obs: 98.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.3 / Redundancy: 12 % / Biso Wilson estimate: 118.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 21.9
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 12 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1419 / Rsym value: 0.787 / % possible all: 97.5

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Processing

Software
NameClassification
HKL-2000data collection
DMmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RHZ

1rhz


Resolution: 3.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 2.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.317 538 -from 1RHZ
Rwork0.301 ---
all-14594 --
obs-10303 70.6 %-
Displacement parametersBiso mean: -0.367 Å2
Baniso -1Baniso -2Baniso -3
1--1.572 Å20 Å20 Å2
2--9.895 Å20 Å2
3----8.323 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 0 0 4052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
3.5-3.660.4219260.4045X-RAY DIFFRACTION397
3.85-4.090.3147420.3077X-RAY DIFFRACTION906
4.09-4.410.3227630.3055X-RAY DIFFRACTION1155
4.41-4.850.3398830.2994X-RAY DIFFRACTION1436
4.85-5.550.3592930.3234X-RAY DIFFRACTION1705
5.55-6.990.411810.3227X-RAY DIFFRACTION1775

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