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- PDB-2cnw: GDPALF4 complex of the SRP GTPases Ffh and FtsY -

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Basic information

Entry
Database: PDB / ID: 2cnw
TitleGDPALF4 complex of the SRP GTPases Ffh and FtsY
Components
  • CELL DIVISION PROTEIN FTSY
  • SIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsSIGNAL RECOGNITION / INNER MEMBRANE / MEMBRANE TARGETING / NUCLEOTIDE-BINDING / GDP- ALUMINUM FLUORIDE / SIGNAL RECOGNITION PARTICLE / RNA-BINDING / GTP-BINDING / CELL DIVISION / SIGNAL SEQUENCE RECOGNITION / SRP / FFH / FTSY / GTPASE / MEMBRANE / CELL CYCLE / CELL DIVISION-COMPLEX
Function / homology
Function and homology information


signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm
Similarity search - Function
Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle ...Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFocia, P.J. / Gawronski-Salerno, J. / Coon V, J.S. / Freymann, D.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of a Gdp:Alf(4) Complex of the Srp Gtpases Ffh and Ftsy, and Identification of a Peripheral Nucleotide Interaction Site.
Authors: Focia, P.J. / Gawronski-Salerno, J. / Coon V, J.S. / Freymann, D.M.
History
DepositionMay 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SIGNAL RECOGNITION PARTICLE PROTEIN
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: CELL DIVISION PROTEIN FTSY
E: CELL DIVISION PROTEIN FTSY
F: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,70727
Polymers189,1956
Non-polymers4,51321
Water11,187621
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
D: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5699
Polymers63,0652
Non-polymers1,5047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
E: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5699
Polymers63,0652
Non-polymers1,5047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SIGNAL RECOGNITION PARTICLE PROTEIN
F: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5699
Polymers63,0652
Non-polymers1,5047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)188.686, 188.686, 44.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.51089, -0.85951, 0.01493), (-0.85964, -0.51085, 0.007), (0.00161, -0.01641, -0.99986)0.99852, -109.08392, 29.65934
2given(-0.50481, -0.86321, 0.00672), (0.86323, -0.50481, 0.00199), (0.00167, 0.00681, 0.99998)-94.2154, -54.88711, -12.41887

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / FFH / FIFTY-FOUR HOMOLOG


Mass: 32300.371 Da / Num. of mol.: 3 / Fragment: NG DOMAIN RESIDUES 1-293
Source method: isolated from a genetically manipulated source
Details: GDP, ALF4, GMP / Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PJGS3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-2(DE3) / References: UniProt: O07347
#2: Protein CELL DIVISION PROTEIN FTSY / FTSY


Mass: 30764.586 Da / Num. of mol.: 3 / Fragment: RESIDUES 20-303
Source method: isolated from a genetically manipulated source
Details: GDP, ALF4, GMP / Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PJGS3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-2(DE3) / References: UniProt: P83749

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Non-polymers , 5 types, 642 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST 19 RESIDUES PRESENT IN THE UNP ENTRY P83749 WERE DELETED IN CHAINS D, E AND F.

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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: 2.35 Å3/Da / Density % sol: 47.23 %
Crystal growpH: 8.5 / Details: 0.1M TRIS-HCL (PH 8.5), 25% (W/V) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97625
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.39→14.9 Å / Num. obs: 287923 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OKK

1okk


Resolution: 2.39→14.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.447 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.505 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THIRTY THREE GLUTAMATE SIDECHAINS A53, A150, A173, A174, A207, A285, B46, B53, B57, B84, B150, B174, B B285, C11, C57, C84, C150, C173, C196, C201, C207, C285, D99, D D245, E151, E165, E204, ...Details: THIRTY THREE GLUTAMATE SIDECHAINS A53, A150, A173, A174, A207, A285, B46, B53, B57, B84, B150, B174, B B285, C11, C57, C84, C150, C173, C196, C201, C207, C285, D99, D D245, E151, E165, E204, E245, F151, F165, F245 EXHIBIT EVIDENCE RADIATION DAMAGE AND THEIR CARBOXYLATE GROUP CD-OE1-OE2 ATOMS A MODELED AT 0.5 OCCUPANCY. ASPARTATE E79 ALSO EXHIBITS EVIDENCE RADIATION DAMAGE AND CARBOXYLATE GROUP ATOMS CG-OD1-OD2 ARE MOD AT 0.5 OCCUPANCY. WATERS THAT ARE IN CHAINS A, B, C, D, E AND F THE NUCLEOPHILIC AND METAL COORDINATING WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3522 5 %RANDOM
Rwork0.183 ---
obs0.186 66478 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.39→14.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12920 0 276 621 13817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2852.0318288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35951704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14823.636550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.224152452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.75915131
X-RAY DIFFRACTIONr_chiral_restr0.0750.22063
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029879
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.26595
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.29222
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2893
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.030.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.58714
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.975213464
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37735476
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2624.54818
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 222 -
Rwork0.217 4857 -
obs--99.88 %

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