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

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Basic information

Entry
Database: PDB / ID: 1rhz
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: 3.5 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, W.M. / Collinson, I. / Modis, Y. / Hartmann, E. / Harrison, S.C. / Rapoport, T.A.
History
DepositionNov 15, 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 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)61,9013
Polymers61,9013
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-65 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.746, 149.361, 79.475
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 Preprotein translocase secY subunit


Mass: 47482.891 Da / Num. of mol.: 1
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: 4.44 Å3/Da / Density % sol: 72.32 %
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: NSLS / Beamline: X25 / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 3.5→10 Å / Num. all: 13799 / Num. obs: 13601 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08 / Net I/σ(I): 30.9
Reflection shellResolution: 3.5→3.7 Å / Mean I/σ(I) obs: 2.74 / Num. unique all: 2010 / Rsym value: 0.67 / % possible all: 92.5
Reflection
*PLUS
Num. obs: 14439 / % possible obs: 98.4 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.63 Å / % possible obs: 89.6 % / Num. unique obs: 1291 / Rmerge(I) obs: 0.67

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→9.99 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 845652.81 / Data cutoff high rms absF: 845652.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.33 669 4.9 %RANDOM
Rwork0.254 ---
obs0.254 13601 98.6 %-
all-13601 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.707 Å2 / ksol: 0.272543 e/Å3
Displacement parametersBiso mean: 122.4 Å2
Baniso -1Baniso -2Baniso -3
1--46.89 Å20 Å20 Å2
2--63.6 Å20 Å2
3----16.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.79 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 3.5→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 0 0 4090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.71 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 99 4.7 %
Rwork0.383 2010 -
obs--92.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 3.5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.334
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Lowest resolution: 3.63 Å

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