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- PDB-5eul: Structure of the SecA-SecY complex with a translocating polypepti... -

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Basic information

Entry
Database: PDB / ID: 5eul
TitleStructure of the SecA-SecY complex with a translocating polypeptide substrate
Components
  • (Protein translocase subunit ...) x 2
  • AYC08
  • Preprotein translocase SecE subunit
KeywordsPROTEIN TRANSPORT / SecY / SecA / ATPase / channel
Function / homology
Function and homology information


protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein secretion / protein transmembrane transporter activity / protein targeting / membrane raft ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein secretion / protein transmembrane transporter activity / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / 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, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop 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, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / HEXATANTALUM DODECABROMIDE / Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
Geobacillus thermodenitrificans (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsLi, L. / Park, E. / Ling, J. / Ingram, J. / Ploegh, H. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
CitationJournal: Nature / Year: 2016
Title: Crystal structure of a substrate-engaged SecY protein-translocation channel.
Authors: Li, L. / Park, E. / Ling, J. / Ingram, J. / Ploegh, H. / Rapoport, T.A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit SecA, Insertion Peptide Chimera
Y: Protein translocase subunit SecY
E: Preprotein translocase SecE subunit
V: AYC08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,17225
Polymers163,8534
Non-polymers37,31921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22960 Å2
ΔGint-131 kcal/mol
Surface area60260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.798, 127.798, 554.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein translocase subunit ... , 2 types, 2 molecules AY

#1: Protein Protein translocase subunit SecA, Insertion Peptide Chimera


Mass: 94360.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Bacillus subtilis (bacteria)
Strain: 168 / Gene: secA, div+, BSU35300 / Production host: Escherichia coli (E. coli) / References: UniProt: P28366
#2: Protein Protein translocase subunit SecY


Mass: 46768.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: secY, GTNG_0125 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJK8

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Protein / Antibody , 2 types, 2 molecules EV

#3: Protein Preprotein translocase SecE subunit


Mass: 8249.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: GTNG_0091 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJH4
#4: Antibody AYC08


Mass: 14475.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 21 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br12Ta6

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Details

Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21-24% polyethylene glycol 1500, 100mM Tris-HCl pH8.5, 50-100 mM MgAc2, 2% 2-methyl-2,4-pentandiol
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 3.7→54 Å / Num. obs: 53847 / % possible obs: 99 % / Redundancy: 10.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.3
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.7→53.852 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 42.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3148 2754 5.11 %Random selection
Rwork0.2952 ---
obs0.2962 53845 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→53.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10155 0 356 0 10511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611001
X-RAY DIFFRACTIONf_angle_d0.99417211
X-RAY DIFFRACTIONf_dihedral_angle_d16.9146339
X-RAY DIFFRACTIONf_chiral_restr0.0541607
X-RAY DIFFRACTIONf_plane_restr0.0051778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.76380.45111510.422584X-RAY DIFFRACTION100
3.7638-3.83230.44571330.41212518X-RAY DIFFRACTION100
3.8323-3.9060.431460.40552576X-RAY DIFFRACTION100
3.906-3.98570.40841480.39372581X-RAY DIFFRACTION100
3.9857-4.07230.45461310.37922513X-RAY DIFFRACTION99
4.0723-4.1670.38551200.35972554X-RAY DIFFRACTION99
4.167-4.27120.36821450.34462569X-RAY DIFFRACTION99
4.2712-4.38660.42131380.30842546X-RAY DIFFRACTION99
4.3866-4.51560.33691640.29152499X-RAY DIFFRACTION99
4.5156-4.66130.30661050.28552551X-RAY DIFFRACTION99
4.6613-4.82780.32681500.28532523X-RAY DIFFRACTION99
4.8278-5.02090.33931150.29172566X-RAY DIFFRACTION99
5.0209-5.24930.39841420.29372555X-RAY DIFFRACTION100
5.2493-5.52580.32571540.29512562X-RAY DIFFRACTION100
5.5258-5.87160.37281260.29662570X-RAY DIFFRACTION100
5.8716-6.32430.36891340.2922578X-RAY DIFFRACTION100
6.3243-6.95950.35021280.25752552X-RAY DIFFRACTION100
6.9595-7.96380.28541210.22472605X-RAY DIFFRACTION100
7.9638-10.0230.21291370.21172561X-RAY DIFFRACTION100
10.023-53.8580.30971660.33862528X-RAY DIFFRACTION100

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