[English] 日本語
Yorodumi
- PDB-2ffh: THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ffh
TitleTHE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS
ComponentsPROTEIN (FFH)
KeywordsPROTEIN TRANSPORT / FFH / SRP54 / SIGNAL RECOGNITION PARTICLE / GTPASE / M DOMAIN / RNA-BINDING / SIGNAL SEQUENCE-BINDING / HELIX-TURN-HELIX / PROTEIN TARGETING
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-domain / 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 subunit, M-domain / 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 / 434 Repressor (Amino-terminal 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKeenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the signal sequence binding subunit of the signal recognition particle.
Authors: Keenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M.
#1: Journal: Nature / Year: 1997
Title: Structure of the Conserved GTPase Domain of the Signal Recognition Particle.
Authors: Freymann, D.M. / Keenan, R.J. / Stroud, R.M. / Walter, P.
History
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,52122
Polymers140,4343
Non-polymers2,08719
Water0
1
A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4707
Polymers46,8111
Non-polymers6586
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3576
Polymers46,8111
Non-polymers5465
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6949
Polymers46,8111
Non-polymers8838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,56366
Polymers421,3039
Non-polymers6,26057
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32770 Å2
ΔGint-551 kcal/mol
Surface area161060 Å2
MethodPISA
5
A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
B: PROTEIN (FFH)
C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,04244
Polymers280,8696
Non-polymers4,17438
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area27280 Å2
ΔGint-410 kcal/mol
Surface area101500 Å2
MethodPISA
6
C: PROTEIN (FFH)
hetero molecules

C: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,04244
Polymers280,8696
Non-polymers4,17438
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation5_566x-y,-y+1,-z+11
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation6_656-x+1,-x+y,-z+11
Buried area13980 Å2
ΔGint-328 kcal/mol
Surface area115240 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-168 kcal/mol
Surface area54650 Å2
MethodPISA
8
C: PROTEIN (FFH)
hetero molecules

C: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38918
Polymers93,6232
Non-polymers1,76616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4280 Å2
ΔGint-112 kcal/mol
Surface area38630 Å2
MethodPISA
9
B: PROTEIN (FFH)
hetero molecules

A: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82713
Polymers93,6232
Non-polymers1,20411
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3660 Å2
ΔGint-92 kcal/mol
Surface area39270 Å2
MethodPISA
10
C: PROTEIN (FFH)
hetero molecules

B: PROTEIN (FFH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,05215
Polymers93,6232
Non-polymers1,42913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area2570 Å2
ΔGint-97 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.050, 195.050, 335.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe bacterial SRP contains one molecule of Ffh bound to one molecule of SRP RNA.

-
Components

#1: Protein PROTEIN (FFH) / FIFTY-FOUR HOMOLOG / P48


Mass: 46811.449 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-425 / Mutation: A48T
Source method: isolated from a genetically manipulated source
Details: THE EXPRESSION INSERT WAS GENERATED BY PCR / Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSE / References: UniProt: O07347
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL ...Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
25 mMHEPES1drop
31.2 M1reservoirNaOAc
40.1 MTris-HCl1reservoir
5120 mM1reservoirCdSO4
620 mMlithium dodecyl sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jul 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 40702 / Num. obs: 36791 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 3.2→3.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3914 / % possible all: 79.6
Reflection shell
*PLUS
% possible obs: 79.6 %

-
Processing

Software
NameVersionClassification
CCP4model building
RAVEmodel building
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RAVEphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FFH

1ffh


Resolution: 3.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined using the maximum likelihood target with individual b-factor refinement and bulk solvent correction.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1862 5.1 %Random
Rwork0.257 ---
all-40702 --
obs-36791 90.4 %-
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9453 0 31 0 9484
Refine LS restraints NCSNCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING ...NCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING THE FINAL STAGES OF REBUILDING AND REFINEMENT, NCS RESTRAINTS WERE RELAXED FOR RESIDUES 271-279 (THE CLOSING LOOP), 295-307 (HINGE) AND 345-356 (C-TERMINAL HALF OF THE FINGER LOOP), WHICH ARE INVOLVED IN EITHER CRYSTALLOGRAPHIC OR NON- CRYSTALLOGRAPHIC PACKING CONTACTS.
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

+
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