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- PDB-6nep: Structure of human PACRG-MEIG1 complex -

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Basic information

Entry
Database: PDB / ID: 6nep
TitleStructure of human PACRG-MEIG1 complex
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 / flagellated sperm motility / glial cell projection / spermatid development / cellular response to unfolded protein / alpha-tubulin binding ...manchette assembly / axonemal B tubule inner sheath / sperm axoneme assembly / axonemal microtubule / manchette / flagellated sperm motility / glial cell projection / spermatid development / cellular response to unfolded protein / alpha-tubulin binding / beta-tubulin binding / heat shock protein binding / sperm midpiece / Hsp70 protein binding / Hsp90 protein binding / G protein-coupled receptor binding / intracellular protein localization / protein-folding chaperone binding / actin binding / cell body / 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
PHOSPHATE ION / Meiosis expressed gene 1 protein homolog / Parkin coregulated gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09762493085 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
DepositionDec 18, 2018Deposition 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 1.2Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)33,6564
Polymers33,5252
Non-polymers1302
Water1,33374
1
A: Parkin coregulated gene protein
hetero molecules

B: Meiosis expressed gene 1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6564
Polymers33,5252
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+3/41
Buried area1190 Å2
ΔGint-25 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.371, 67.371, 159.716
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

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


Mass: 22298.510 Da / Num. of mol.: 1 / Mutation: Deletion 1-69, Y189PHI
Source method: isolated from a genetically manipulated source
Details: Generated from GST-fusion, and cleaved with 3C protease, leaving a GPLGS linker at N-terminus. Tyrosine 189 was mutated in Iodo-phenylalanine in order to incorporate anomalous scattering atom for phasing.
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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 18%PEG8K, 60mM KHPO4, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.476 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.476 Å / Relative weight: 1
ReflectionResolution: 2.09→47.64 Å / Num. obs: 253322 / % possible obs: 99.8 % / Redundancy: 11.3 % / Biso Wilson estimate: 43.8362539878 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.7
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 9944 / CC1/2: 0.73 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless1.12_2829data scaling
PHENIXphasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.09762493085→47.6384909553 Å / SU ML: 0.281412881549 / Cross valid method: THROUGHOUT / σ(F): 0.360717156976 / Phase error: 31.4403924482
RfactorNum. reflection% reflection
Rfree0.249329110804 2049 5.0032964618 %
Rwork0.228564071678 --
obs0.22961406499 40953 99.5333576376 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.9849979618 Å2
Refinement stepCycle: LAST / Resolution: 2.09762493085→47.6384909553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 6 74 2156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008891663630152133
X-RAY DIFFRACTIONf_angle_d0.9530755004962890
X-RAY DIFFRACTIONf_chiral_restr0.290988541613308
X-RAY DIFFRACTIONf_plane_restr0.0052816449021370
X-RAY DIFFRACTIONf_dihedral_angle_d22.0427649872777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0976-2.14640.3395610606261180.3591887744912520X-RAY DIFFRACTION96.242247355
2.1464-2.20010.4291723412761370.3571471468762596X-RAY DIFFRACTION99.4541484716
2.2001-2.25960.3627753158431160.3463514501432604X-RAY DIFFRACTION99.1615020051
2.2596-2.32610.4336283168441310.3163573622882601X-RAY DIFFRACTION98.8780311256
2.3261-2.40110.3290318931521260.3172552572382584X-RAY DIFFRACTION99.7056659308
2.4011-2.4870.3194668430571670.2947826226892585X-RAY DIFFRACTION99.891107078
2.487-2.58650.352548310061400.2997513219232629X-RAY DIFFRACTION100
2.5865-2.70420.2367862538441410.2807295032312566X-RAY DIFFRACTION99.9630723781
2.7042-2.84680.3354196323591440.2648753298912593X-RAY DIFFRACTION99.9634769905
2.8468-3.02510.2553777360141480.2529224374182594X-RAY DIFFRACTION100
3.0251-3.25860.2794551721761400.2434643946832597X-RAY DIFFRACTION99.9634769905
3.2586-3.58650.2525216938261540.2159401774042592X-RAY DIFFRACTION99.9272197962
3.5865-4.10520.1937873651581200.1919454695142622X-RAY DIFFRACTION100
4.1052-5.17110.1681584088921180.1713413845362637X-RAY DIFFRACTION100
5.1711-47.65080.2153114760661490.1969829473452584X-RAY DIFFRACTION99.8538545853

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