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- PDB-2zjs: Crystal Structure of SecYE translocon from Thermus thermophilus w... -

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Basic information

Entry
Database: PDB / ID: 2zjs
TitleCrystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment
Components
  • Fab56 (heavy chain)
  • Fab56 (light chain)
  • Preprotein translocase SecE subunit
  • Preprotein translocase SecY subunit
KeywordsPROTEIN TRANSPORT/IMMUNE SYSTEM / Translocon / Sec / Protein-conducting-channel / Membrane / Protein transport / Translocation / Transmembrane / Transport / PROTEIN TRANSPORT-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein secretion / protein transmembrane transporter activity / protein targeting / plasma membrane
Similarity search - Function
Preprotein translocase secy subunit / Preprotein translocase SecY subunit / SecY subunit domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit ...Preprotein translocase secy subunit / Preprotein translocase SecY subunit / SecY subunit domain / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecY / Protein translocase subunit SecE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsTsukazaki, T. / Mori, H. / Fukai, S. / Ishitani, R. / Perederina, A. / Vassylyev, D.G. / Ito, K. / Nureki, O.
CitationJournal: Nature / Year: 2008
Title: Conformational transition of Sec machinery inferred from bacterial SecYE structures
Authors: Tsukazaki, T. / Mori, H. / Fukai, S. / Ishitani, R. / Mori, T. / Dohmae, N. / Perederina, A. / Sugita, Y. / Vassylyev, D.G. / Ito, K. / Nureki, O.
History
DepositionMar 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit
H: Fab56 (heavy chain)
L: Fab56 (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3646
Polymers102,2334
Non-polymers1312
Water00
1
Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7813
Polymers54,7162
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Fab56 (heavy chain)
L: Fab56 (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5833
Polymers47,5182
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit
hetero molecules

Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5626
Polymers109,4314
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8340 Å2
ΔGint-207 kcal/mol
Surface area46680 Å2
MethodPISA
5
H: Fab56 (heavy chain)
L: Fab56 (light chain)
hetero molecules

H: Fab56 (heavy chain)
L: Fab56 (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1666
Polymers95,0354
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9280 Å2
ΔGint-119 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.096, 103.073, 78.005
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number5
Space group name H-MC121
DetailsOligomerization of the SecYE(G) complex had been observed in a number of studies.

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Components

#1: Protein Preprotein translocase SecY subunit


Mass: 47643.102 Da / Num. of mol.: 1 / Fragment: residues 1-434 / Mutation: L2V, R252G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP3, UniProt: Q5SHQ8*PLUS
#2: Protein Preprotein translocase SecE subunit


Mass: 7072.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP4, UniProt: P38383*PLUS
#3: Antibody Fab56 (heavy chain)


Mass: 23781.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: hybridoma
#4: Antibody Fab56 (light chain)


Mass: 23736.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: hybridoma
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11% PEG 1500, 0.1M HEPES-Na (pH 7.5), 0.14M ammonium formate, 0.02% n-Dodecyl-beta-D-maltoside, 0.002M zinc acetate, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.97942
SYNCHROTRONPhoton Factory AR-NW12A20.97920,0.97942,0.96418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 4, 2007
ADSC QUANTUM 2102CCDOct 25, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.97921
30.964181
ReflectionResolution: 3.2→48.43 Å / Num. obs: 22585

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD / Resolution: 3.2→48.43 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.91 / SU B: 62.254 / SU ML: 0.475 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 1212 5.1 %RANDOM
Rwork0.24424 ---
obs0.24604 22465 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å23.82 Å2
2--1.58 Å20 Å2
3---5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 2 0 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9559681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6223.463283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.415151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0391537
X-RAY DIFFRACTIONr_chiral_restr0.0820.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23471
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24869
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1730.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0190.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3531.54519
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63627191
X-RAY DIFFRACTIONr_scbond_it0.51432949
X-RAY DIFFRACTIONr_scangle_it0.8994.52490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 92 -
Rwork0.375 1635 -
obs--97.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2481-0.7537-1.46660.41120.05980.7988-0.2413-0.45120.01720.15140.1389-0.21260.15010.19820.1024-0.13710.0807-0.0283-0.1527-0.0486-0.110319.65680.003937.1227
23.7302-0.2317-1.70391.65860.56661.13330.20110.6466-0.1681-0.1346-0.08790.1897-0.2312-0.46-0.1132-0.21690.0998-0.0577-0.0144-0.0023-0.173862.75131.29140.2166
33.40830.8712-1.29020.98820.36372.30740.09410.788-0.1611-0.0567-0.0068-0.0158-0.01460.0477-0.0874-0.15730.07540.01410.0128-0.0404-0.367694.0802-3.393-17.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1YA1 - 4221 - 422
2X-RAY DIFFRACTION1EB12 - 5712 - 57
3X-RAY DIFFRACTION2HC1 - 1201 - 120
4X-RAY DIFFRACTION2LD1 - 1071 - 107
5X-RAY DIFFRACTION3HC121 - 220121 - 220
6X-RAY DIFFRACTION3LD108 - 214108 - 214
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param

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