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

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Basic information

Entry
Database: PDB / ID: 6ndu
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 / beta-tubulin binding / spermatid development / alpha-tubulin binding / cellular response to unfolded protein / sperm midpiece ...manchette assembly / axonemal B tubule inner sheath / sperm axoneme assembly / axonemal microtubule / manchette / beta-tubulin binding / spermatid development / alpha-tubulin binding / cellular response to unfolded protein / sperm midpiece / heat shock protein binding / Hsp70 protein binding / G protein-coupled receptor binding / Hsp90 protein binding / protein localization / actin binding / protein-folding chaperone 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 14, 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 1.2Oct 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)33,5464
Polymers33,4152
Non-polymers1302
Water1,38777
1
A: Parkin coregulated gene protein
hetero molecules

B: Meiosis expressed gene 1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5464
Polymers33,4152
Non-polymers1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+3/41
Buried area1130 Å2
ΔGint-24 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.297, 67.297, 158.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 22188.613 Da / Num. of mol.: 1 / Mutation: Deletion 1-69
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.
Source: (gene. exp.) Homo sapiens (human) / Gene: PACRG, GLUP / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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) / Strain (production host): BL21(DE3) / References: UniProt: Q5JSS6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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.: 77 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 8000, 0.04 M KH2PO4, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→47.59 Å / Num. obs: 22042 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 47.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.166.71.30317520.6220.5361.411100
8.91-47.595.10.0283630.9990.0140.03299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.25 Å47.59 Å
Translation2.25 Å47.59 Å

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
XDSVERSION Nov 1, 2016data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NEP

6nep


Resolution: 2.1→47.586 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2272 1112 5.07 %
Rwork0.19 --
obs0.1919 21950 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.9 Å2 / Biso mean: 60.0665 Å2 / Biso min: 30.35 Å2
Refinement stepCycle: final / Resolution: 2.1→47.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 6 77 2132
Biso mean--93.86 58.41 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082144
X-RAY DIFFRACTIONf_angle_d1.0772915
X-RAY DIFFRACTIONf_chiral_restr0.042313
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d13.922781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.19560.31161280.273925252653100
2.1956-2.31140.38191240.31652550267499
2.3114-2.45620.27381470.233825422689100
2.4562-2.64580.28341430.233925732716100
2.6458-2.91210.29121440.224425792723100
2.9121-3.33340.25571410.203126052746100
3.3334-4.19930.18761350.16412658279399
4.1993-47.59840.19161500.163528062956100
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)
11.855-0.0511.29452.68771.07448.1429-0.27270.240.0766-0.16980.1902-0.1514-0.60940.20520.0680.2702-0.0661-0.0160.40160.02910.31511.200727.839143.2253
23.4612-0.424-0.69193.6912-1.14424.9289-0.4434-0.20340.40340.3574-0.2025-0.8465-0.65890.64990.63510.44950.0162-0.17770.52660.06840.661131.900426.226462.3575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 255 )A69 - 255
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 88 )B5 - 88

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