[English] 日本語
Yorodumi
- PDB-2cnw: GDPALF4 complex of the SRP GTPases Ffh and FtsY -

+
Open data


ID or keywords:

Loading...

-
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 / signal recognition particle binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more