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- PDB-3din: Crystal structure of the protein-translocation complex formed by ... -

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Basic information

Entry
Database: PDB / ID: 3din
TitleCrystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase
Components
  • (Preprotein translocase subunit ...) x 3
  • Protein translocase subunit secA
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / protein translocation / ATPase / ATP-binding / Inner membrane / Nucleotide-binding / Transport / Transmembrane
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 / protein transmembrane transporter activity / protein secretion / protein targeting / membrane => GO:0016020 / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecA P-loop domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecA P-loop domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / 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 / Helicase conserved C-terminal domain / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Protein-export membrane protein SecG / Protein-export membrane protein SecG / Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
Thermotoga sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 4.5 Å
AuthorsZimmer, J. / Nam, Y. / Rapoport, T.A.
CitationJournal: Nature / Year: 2008
Title: Structure of a complex of the ATPase SecA and the protein-translocation channel.
Authors: Zimmer, J. / Nam, Y. / Rapoport, T.A.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit secA
C: Preprotein translocase subunit SecY
D: Preprotein translocase subunit secE
E: Preprotein translocase subunit SecG
B: Protein translocase subunit secA
F: Preprotein translocase subunit SecY
G: Preprotein translocase subunit secE
H: Preprotein translocase subunit SecG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,90814
Polymers328,8738
Non-polymers1,0356
Water0
1
A: Protein translocase subunit secA
C: Preprotein translocase subunit SecY
D: Preprotein translocase subunit secE
E: Preprotein translocase subunit SecG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9547
Polymers164,4374
Non-polymers5183
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-93.7 kcal/mol
Surface area68920 Å2
MethodPISA
2
B: Protein translocase subunit secA
F: Preprotein translocase subunit SecY
G: Preprotein translocase subunit secE
H: Preprotein translocase subunit SecG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9547
Polymers164,4374
Non-polymers5183
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-94.4 kcal/mol
Surface area68900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.616, 156.003, 358.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein translocase subunit secA


Mass: 100643.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secA, TM_1578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1R4

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Preprotein translocase subunit ... , 3 types, 6 molecules CFDGEH

#2: Protein Preprotein translocase subunit SecY


Mass: 48217.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secY, TM_1480 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1I9
#3: Protein Preprotein translocase subunit secE


Mass: 7322.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secE, TM_0452 / Production host: Escherichia coli (E. coli) / References: UniProt: P35874
#4: Protein Preprotein translocase subunit SecG


Mass: 8251.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga sp. (bacteria) / Strain: RQ2 / Gene: secG, TRQ2_0456 / Production host: Escherichia coli (E. coli) / References: UniProt: B1L914, UniProt: A0A0F6AK20*PLUS

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Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3

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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: 4.32 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 20% PEG 3350, 200mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9795
SYNCHROTRONAPS 24-ID-C20.9795
SYNCHROTRONNSLS X29A30.9795
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDAug 15, 2007Cryogenically cooled first crystal, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
ADSC QUANTUM 3152CCDOct 17, 2007Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry
ADSC QUANTUM 3153CCDFeb 29, 2008sagitally bent second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystalSINGLE WAVELENGTHMx-ray1
2Cryogenically cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
3Cryogenically cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 34733 / % possible obs: 97.7 % / Redundancy: 11.6 % / Rsym value: 0.065 / Net I/σ(I): 16.1
Reflection shellResolution: 4.5→4.77 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.85 / % possible all: 89.7

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
DMphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TF2

1tf2


Resolution: 4.5→15 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.303 3269 10 %RANDOM
Rwork0.279 ---
obs0.279 34733 97.7 %-
all-34733 --
Displacement parametersBiso mean: 358.2 Å2
Baniso -1Baniso -2Baniso -3
1-9.68 Å20 Å20 Å2
2--13.17 Å20 Å2
3----22.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.11 Å1 Å
Luzzati d res low-5 Å
Luzzati sigma a3.22 Å2.24 Å
Refinement stepCycle: LAST / Resolution: 4.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21304 0 64 0 21368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
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: 4.5→4.77 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 475 9.6 %
Rwork0.45 4452 -
obs--88.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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