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- PDB-1rh5: The structure of a protein conducting channel -

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Basic information

Entry
Database: PDB / ID: 1rh5
TitleThe structure of a protein conducting channel
Components
  • Preprotein translocase secE subunit
  • Preprotein translocase secY subunit
  • SecBeta
KeywordsPROTEIN TRANSPORT / Protein translocation / SecY / Membrane Protein / Protein Channels
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 / SAD / Resolution: 3.2 Å
Authorsvan den Berg, B. / Clemons Jr., W.M. / Collinson, I. / Modis, Y. / Hartmann, E. / Harrison, S.C. / Rapoport, T.A.
CitationJournal: Nature / Year: 2004
Title: X-ray structure of a protein-conducting channel
Authors: van den Berg, B. / Clemons Jr., W.M. / Collinson, I. / Modis, Y. / Hartmann, E. / Harrison, S.C. / Rapoport, T.A.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999sequence No suitable sequence database reference was available for chain C at the time of ...sequence No suitable sequence database reference was available for chain C at the time of processing this file.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,9313
Polymers61,9313
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-67 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.930, 156.650, 69.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsBiological assembly consists of a tetramer.

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Components

#1: Protein Preprotein translocase secY subunit


Mass: 47512.879 Da / Num. of mol.: 1 / Mutation: R422K, T423V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: SECY, MJ0478 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q60175
#2: Protein Preprotein translocase secE subunit / 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, MJ0371 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q57817
#3: Protein SecBeta


Mass: 5967.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P60460*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: 4.54 Å3/Da / Density % sol: 72.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: Peg 400, Glycine buffer, glycerol, sodium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 9.5 / PH range high: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein1drop
250-55 %PEG4001reservoir
350 mMglycine1reservoirpH9.0-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2003
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→10 Å / Num. all: 18818 / Num. obs: 17396 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.05 / Net I/σ(I): 26.9
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 1439 / Rsym value: 0.44 / % possible all: 76.1
Reflection
*PLUS
Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 76.1 % / Num. unique obs: 1439 / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 348802.96 / Data cutoff high rms absF: 348802.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1648 9.8 %RANDOM
Rwork0.242 ---
obs0.242 16736 90.1 %-
all-18559 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.7652 Å2 / ksol: 0.309755 e/Å3
Displacement parametersBiso mean: 97.8 Å2
Baniso -1Baniso -2Baniso -3
1--19.24 Å20 Å20 Å2
2---7.36 Å20 Å2
3---26.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 0 0 3852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 3.2→3.39 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 220 10.1 %
Rwork0.375 1968 -
obs--72.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Lowest resolution: 3.31 Å / Rfactor Rfree: 0.442 / Rfactor Rwork: 0.414

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