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- PDB-3kbl: Crystal structure of the GLD-1 homodimerization domain from Caeno... -

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Basic information

Entry
Database: PDB / ID: 3kbl
TitleCrystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans N169A mutant at 2.28 A resolution
ComponentsFemale germline-specific tumor suppressor gld-1
KeywordsPROTEIN BINDING / GLD-1 / N169A MUTANT / QUA1 HOMODIMERIZATION DOMAIN / HELIX-TURN-HELIX MOTIF / HYDROPHOBIC HOMODIMER INTERFACE / PERPENDICULAR STACKING OF PROTOMERS / Developmental protein / Differentiation / Meiosis / Oogenesis / RNA-binding / Translation regulation
Function / homology
Function and homology information


oocyte fate determination / positive regulation of female gonad development / regulation of germ cell proliferation / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of oocyte development / regulation of mRNA splicing, via spliceosome / P granule / post-transcriptional regulation of gene expression / oogenesis / meiotic cell cycle ...oocyte fate determination / positive regulation of female gonad development / regulation of germ cell proliferation / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of oocyte development / regulation of mRNA splicing, via spliceosome / P granule / post-transcriptional regulation of gene expression / oogenesis / meiotic cell cycle / mRNA 3'-UTR binding / mRNA 5'-UTR binding / regulation of gene expression / single-stranded RNA binding / negative regulation of translation / negative regulation of gene expression / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / K Homology domain / K homology RNA-binding domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4010 / STAR protein, homodimerisation region / Homodimerisation region of STAR domain protein / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / K Homology domain, type 1 superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / K Homology domain / K homology RNA-binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Female germline-specific tumor suppressor gld-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsBeuck, C. / Szymczyna, B.R. / Kerkow, D.E. / Carmel, A.B. / Columbus, L. / Stanfield, R.L. / Williamson, J.R.
CitationJournal: Structure / Year: 2010
Title: Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation.
Authors: Beuck, C. / Szymczyna, B.R. / Kerkow, D.E. / Carmel, A.B. / Columbus, L. / Stanfield, R.L. / Williamson, J.R.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Female germline-specific tumor suppressor gld-1
B: Female germline-specific tumor suppressor gld-1
C: Female germline-specific tumor suppressor gld-1
D: Female germline-specific tumor suppressor gld-1


Theoretical massNumber of molelcules
Total (without water)27,3754
Polymers27,3754
Non-polymers00
Water68538
1
A: Female germline-specific tumor suppressor gld-1
B: Female germline-specific tumor suppressor gld-1


Theoretical massNumber of molelcules
Total (without water)13,6882
Polymers13,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area6920 Å2
MethodPISA
2
C: Female germline-specific tumor suppressor gld-1
D: Female germline-specific tumor suppressor gld-1


Theoretical massNumber of molelcules
Total (without water)13,6882
Polymers13,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-10 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.406, 42.300, 156.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Female germline-specific tumor suppressor gld-1 / Defective in germ line development protein 1


Mass: 6843.811 Da / Num. of mol.: 4 / Fragment: Qua1 homodimerization domain / Mutation: N169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-1, T23G11.3 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q17339
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES-Na, PEG 200, PEG 3000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2008
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 11001 / Num. obs: 11001 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.065 / Χ2: 1.011 / Net I/σ(I): 12.1
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.37 / Num. unique all: 492 / Rsym value: 0.26 / Χ2: 0.971 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CS-Rosetta model of wildtype construct with sidechain of N169 changed to A to account for mutation

Resolution: 2.28→37.192 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.45 / σ(F): 1.35 / Stereochemistry target values: ML
Details: TLS refinement with each monomer chain used as independent TLS unit
RfactorNum. reflection% reflectionSelection details
Rfree0.264 552 5.04 %RANDOM
Rwork0.195 ---
obs0.199 10945 99.09 %-
all-10945 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.851 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 130.54 Å2 / Biso mean: 47.775 Å2 / Biso min: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1-8.381 Å20 Å2-0 Å2
2--0.139 Å20 Å2
3----8.52 Å2
Refinement stepCycle: LAST / Resolution: 2.28→37.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 38 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081678
X-RAY DIFFRACTIONf_angle_d1.0112262
X-RAY DIFFRACTIONf_chiral_restr0.063262
X-RAY DIFFRACTIONf_plane_restr0.004286
X-RAY DIFFRACTIONf_dihedral_angle_d15.151620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.5070.2971250.2152464258996
2.507-2.870.2551360.20425972733100
2.87-3.6160.2971390.19725862725100
3.616-37.1970.241520.18427462898100
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)
10.5172-0.8178-0.23590.6034-0.60751.2450.04360.15810.0289-0.0158-0.05890.1248-0.1181-0.1745-0.00040.2639-0.0387-0.00590.29750.01360.296416.3135-1.56332.5933
21.00690.5489-0.10850.3945-0.2320.50960.00390.11390.0914-0.12980.0030.10710.1422-0.1323-0.02940.24070.00220.00020.32580.040.273811.5649-12.083214.6055
30.3740.09980.68890.33650.44981.3899-0.02850.1693-0.0525-0.06540.17770.03110.09030.3042-0.10970.3051-0.0616-0.05320.3508-0.02120.29166.891712.547236.6315
40.264-0.363-0.0495-0.2852-0.19460.45650.1225-0.2307-0.14440.0138-0.0639-0.02210.24260.2237-0.07330.3836-0.0635-0.06970.22690.01110.3034-1.84396.204424.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 195
2X-RAY DIFFRACTION2chain BB-1 - 187
3X-RAY DIFFRACTION3chain CC-1 - 195
4X-RAY DIFFRACTION4chain DD-1 - 187

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