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- PDB-6ucc: Structure of human PACRG-MEIG1 complex (limited proteolysis) -

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Basic information

Entry
Database: PDB / ID: 6ucc
TitleStructure of human PACRG-MEIG1 complex (limited proteolysis)
Components
  • Meiosis expressed gene 1 protein homolog
  • Parkin coregulated gene protein
KeywordsSTRUCTURAL PROTEIN / Microtubule / axoneme / primary cilia / flagella
Function / homology
Function and homology information


manchette assembly / axonemal B tubule inner sheath / sperm axoneme assembly / axonemal microtubule / manchette / beta-tubulin binding / alpha-tubulin binding / spermatid development / cellular response to unfolded protein / sperm midpiece ...manchette assembly / axonemal B tubule inner sheath / sperm axoneme assembly / axonemal microtubule / manchette / beta-tubulin binding / alpha-tubulin binding / spermatid development / cellular response to unfolded protein / sperm midpiece / Hsp70 protein binding / heat shock protein binding / G protein-coupled receptor binding / Hsp90 protein binding / protein localization / actin binding / cell body / protein-folding chaperone binding / vesicle / neuron projection / ubiquitin protein ligase binding / nucleus / cytosol
Similarity search - Function
Meiosis-expressed gene 1 protein / Meiosis-expressed / Parkin co-regulated protein / Parkin co-regulated protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Meiosis expressed gene 1 protein homolog / Parkin coregulated gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKhan, N. / Croteau, N. / Pelletier, D. / Veyron, S. / Trempe, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)950-229792 X-239354 Canada
CitationJournal: Biorxiv / Year: 2019
Title: Crystal structure of human PACRG in complex with MEIG1
Authors: Khan, N. / Pelletier, D. / Veyron, S. / Croteau, N. / Ichikawa, M. / Black, C. / Khalifa, A.A.Z. / Chaaban, S. / Kurinov, I. / Brouhard, G. / Bui, K.H. / Trempe, J.F.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parkin coregulated gene protein
B: Meiosis expressed gene 1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9745
Polymers40,5792
Non-polymers3953
Water37821
1
B: Meiosis expressed gene 1 protein homolog
hetero molecules

A: Parkin coregulated gene protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9745
Polymers40,5792
Non-polymers3953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area1200 Å2
ΔGint-13 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.854, 66.854, 158.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Parkin coregulated gene protein / Molecular chaperone/chaperonin-binding protein / PARK2 coregulated gene protein


Mass: 29352.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Generated by limited proteolysis using subtilisin / Source: (gene. exp.) Homo sapiens (human) / Gene: PACRG, GLUP / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96M98
#2: Protein Meiosis expressed gene 1 protein homolog


Mass: 11226.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full-length MEIG1 expressed as His-tagged protein, cleaved with the 3C protease, leaving GPLGS at N-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JSS6

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Non-polymers , 4 types, 24 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 20% glycerol, 0.2M KH2PO4, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→47.27 Å / Num. obs: 11793 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 54.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.082 / Rrim(I) all: 0.295 / Χ2: 1 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.868 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1395 / CC1/2: 0.557 / Rpim(I) all: 0.871 / Rrim(I) all: 3.131 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NDU

6ndu


Resolution: 2.6→47.27 Å / SU ML: 0.347 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 634 5.4 %
Rwork0.2136 11097 -
obs0.2173 11731 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 25 21 2106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752142
X-RAY DIFFRACTIONf_angle_d0.88342898
X-RAY DIFFRACTIONf_chiral_restr0.0537309
X-RAY DIFFRACTIONf_plane_restr0.0064369
X-RAY DIFFRACTIONf_dihedral_angle_d21.9945781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.36281280.29982151X-RAY DIFFRACTION99.87
2.8-3.080.29231180.2672172X-RAY DIFFRACTION99.91
3.08-3.530.28721170.22332204X-RAY DIFFRACTION99.91
3.53-4.450.2551350.18392207X-RAY DIFFRACTION100
4.45-47.270.28771360.20182363X-RAY DIFFRACTION99.96

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