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

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Basic information

Entry
Database: PDB / ID: 2yxr
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 / translocon / 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: 3.6 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: Advisory / 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 57-67 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)60,6243
Polymers60,6243
Non-polymers00
Water00
1
A: Preprotein translocase subunit secY


Theoretical massNumber of molelcules
Total (without water)46,2051
Polymers46,2051
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 area6090 Å2
ΔGint-64 kcal/mol
Surface area28130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.510, 150.360, 79.850
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: 46205.449 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: 4.89 Å3/Da / Density % sol: 74.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 40-55% PEG400, 50mM Glycine-HCl, pH 9.5, 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: 14808 / Num. obs: 14742 / % possible obs: 99.6 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.3 / Redundancy: 8 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 16.8
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 8 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1449 / Rsym value: 0.739 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0026refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RHZ

1rhz


Resolution: 3.6→44.07 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.863 / SU B: 103.673 / SU ML: 0.717 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.8 / σ(I): 3.3 / ESU R Free: 0.976 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33457 465 5.3 %RANDOM
Rwork0.29782 ---
obs0.29972 8359 65.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 105.182 Å2
Baniso -1Baniso -2Baniso -3
1-4.96 Å20 Å20 Å2
2---5.49 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 3.6→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3999 0 0 0 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9895540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15523.023129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.6415726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4631515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022905
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.22261
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22881
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5121.52640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91824162
X-RAY DIFFRACTIONr_scbond_it0.43331655
X-RAY DIFFRACTIONr_scangle_it0.7294.51378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.601→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.518 9 -
Rwork0.319 131 -
obs--14.66 %
Refinement TLS params.Method: refined / Origin x: 19.7141 Å / Origin y: -28.5331 Å / Origin z: -18.2369 Å
111213212223313233
T-0.2704 Å2-0.0395 Å2-0.0037 Å2-0.1607 Å20.0016 Å2---0.3028 Å2
L2.35 °20.3536 °20.4189 °2-1.9442 °2-0.0753 °2--1.7097 °2
S0.0681 Å °0.2729 Å °0.4283 Å °-0.1253 Å °0.0446 Å °0.0137 Å °-0.2427 Å °0.1603 Å °-0.1127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4332 - 423
2X-RAY DIFFRACTION1BB2 - 663 - 67
3X-RAY DIFFRACTION1CC21 - 5221 - 52

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