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- PDB-5w4a: C. japonica N-domain -

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Basic information

Entry
Database: PDB / ID: 5w4a
TitleC. japonica N-domain
ComponentsP-granule scaffold
KeywordsRNA BINDING PROTEIN / P-granule scaffold protein
Function / homologyIMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein / :
Function and homology information
Biological speciesCaenorhabditis japonica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAoki, S.T. / Bingman, C.A. / Kimble, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)K99 HD081208 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2021
Title: C. elegans germ granules require both assembly and localized regulators for mRNA repression.
Authors: Aoki, S.T. / Lynch, T.R. / Crittenden, S.L. / Bingman, C.A. / Wickens, M. / Kimble, J.
History
DepositionJun 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: 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
A: P-granule scaffold
B: P-granule scaffold
C: P-granule scaffold
D: P-granule scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,52427
Polymers97,4894
Non-polymers2,03523
Water15,061836
1
A: P-granule scaffold
C: P-granule scaffold
hetero molecules


  • defined by author
  • Evidence: equilibrium centrifugation, Analytical centrifugation of homolog ran as a dimer, gel filtration, SEC-MALS of homolog ran as a dimer, assay for oligomerization, mutatgenesis of dimer ...Evidence: equilibrium centrifugation, Analytical centrifugation of homolog ran as a dimer, gel filtration, SEC-MALS of homolog ran as a dimer, assay for oligomerization, mutatgenesis of dimer interface created monomers (SEC-MALS)
  • 49.9 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)49,86715
Polymers48,7442
Non-polymers1,12213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P-granule scaffold
D: P-granule scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,65712
Polymers48,7442
Non-polymers91310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.770, 94.670, 72.950
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21A-592-

HOH

31D-541-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
P-granule scaffold


Mass: 24372.131 Da / Num. of mol.: 4 / Fragment: N-domain (UNP residues 1-216)
Source method: isolated from a genetically manipulated source
Details: codon optimized version synthesized for bacterial expression
Source: (gene. exp.) Caenorhabditis japonica (invertebrata) / Plasmid: pET21a / Details (production host): IPTG inducible / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta2 / References: UniProt: H2W791, UniProt: A0A2H2IB89*PLUS

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Non-polymers , 6 types, 859 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Imidazole pH 7.5, 40-45% PEG 400, 1 mM TCEP pH 7.4
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2016 / Details: MD2 Micro Diffractometer
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→30.361 Å / Num. obs: 283749 / % possible obs: 99.77 % / Redundancy: 15.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08108 / Rpim(I) all: 0.01984 / Net I/σ(I): 16.91
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 14301 / CC1/2: 0.662 / Rpim(I) all: 0.357 / % possible all: 99.33

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4D

5w4d


Resolution: 1.5→30.361 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.16
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2915 1.03 %1468
Rwork0.1618 ---
obs0.1622 283749 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→30.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 136 836 7710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097040
X-RAY DIFFRACTIONf_angle_d0.9899463
X-RAY DIFFRACTIONf_dihedral_angle_d10.3234336
X-RAY DIFFRACTIONf_chiral_restr0.051088
X-RAY DIFFRACTIONf_plane_restr0.0061229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52460.37241520.320913172X-RAY DIFFRACTION98
1.5246-1.55090.28861360.287413463X-RAY DIFFRACTION100
1.5509-1.57910.28961350.271813337X-RAY DIFFRACTION100
1.5791-1.60950.27071290.252313299X-RAY DIFFRACTION100
1.6095-1.64230.2991420.23313467X-RAY DIFFRACTION100
1.6423-1.6780.20441300.223813469X-RAY DIFFRACTION100
1.678-1.71710.2751500.207613321X-RAY DIFFRACTION100
1.7171-1.760.22361400.199813432X-RAY DIFFRACTION100
1.76-1.80760.24611440.190813423X-RAY DIFFRACTION100
1.8076-1.86080.22531320.170413247X-RAY DIFFRACTION99
1.8608-1.92080.20461390.165213237X-RAY DIFFRACTION99
1.9208-1.98940.18461390.157213452X-RAY DIFFRACTION100
1.9894-2.06910.15861430.152613349X-RAY DIFFRACTION100
2.0691-2.16320.20371380.143713403X-RAY DIFFRACTION100
2.1632-2.27720.16381360.133813460X-RAY DIFFRACTION100
2.2772-2.41990.16661460.137113356X-RAY DIFFRACTION100
2.4199-2.60660.19421420.141213451X-RAY DIFFRACTION100
2.6066-2.86870.25951260.152113363X-RAY DIFFRACTION100
2.8687-3.28340.19531360.156813436X-RAY DIFFRACTION100
3.2834-4.13510.18911420.146713399X-RAY DIFFRACTION100
4.1351-30.36710.15861380.162413298X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.4193 Å / Origin y: -13.2487 Å / Origin z: 17.9092 Å
111213212223313233
T0.1356 Å2-0.0035 Å2-0.0004 Å2-0.1062 Å2-0.0114 Å2--0.137 Å2
L0.4239 °20.0204 °20.0005 °2-0.2751 °2-0.0731 °2--0.3533 °2
S0.005 Å °-0.0109 Å °0.0263 Å °0.0051 Å °-0.0261 Å °-0.0081 Å °-0.0218 Å °0.0068 Å °-0 Å °
Refinement TLS groupSelection details: all

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