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- PDB-4m8m: Crystal structure of the active dimer of zebrafish PlexinC1 cytop... -

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Basic information

Entry
Database: PDB / ID: 4m8m
TitleCrystal structure of the active dimer of zebrafish PlexinC1 cytoplasmic region
ComponentsGCN4 coiled-coil fused zebrafish PlexinC1
KeywordsSIGNALING PROTEIN / RasGAP-like fold / GAP for Rap GTPases / Rap / Membrane
Function / homology
Function and homology information


semaphorin receptor activity / axon guidance / membrane
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Sema domain / Sema domain superfamily / Sema domain profile. ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / Rho GTPase activation protein / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.307 Å
AuthorsWang, Y. / Pascoe, H.G. / Zhang, X.
CitationJournal: Elife / Year: 2013
Title: Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.
Authors: Wang, Y. / Pascoe, H.G. / Brautigam, C.A. / He, H. / Zhang, X.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GCN4 coiled-coil fused zebrafish PlexinC1
B: GCN4 coiled-coil fused zebrafish PlexinC1


Theoretical massNumber of molelcules
Total (without water)146,2472
Polymers146,2472
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-35 kcal/mol
Surface area54520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.216, 146.100, 209.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GCN4 coiled-coil fused zebrafish PlexinC1


Mass: 73123.688 Da / Num. of mol.: 2
Fragment: zebrafish PlexinC1 cytoplasmic region, UNP residues 456-1056
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Plexin C1, plxnc1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(ArcticExpress) / References: UniProt: Q5RGW1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: 0.1M Bis-Tris propane, pH 9.1, 21% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2013
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 25124 / Num. obs: 24065 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 73.91 Å2 / Rsym value: 0.111 / Net I/σ(I): 19.7
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1211 / Rsym value: 0.868 / % possible all: 79.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 3.307→44.164 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 1071 5.08 %
Rwork0.2255 --
obs0.2283 21087 83.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.307→44.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8871 0 0 17 8888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059034
X-RAY DIFFRACTIONf_angle_d0.85112233
X-RAY DIFFRACTIONf_dihedral_angle_d13.2963217
X-RAY DIFFRACTIONf_chiral_restr0.0591437
X-RAY DIFFRACTIONf_plane_restr0.0031545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.307-3.45750.2917570.2901957X-RAY DIFFRACTION33
3.4575-3.63970.2979950.27081715X-RAY DIFFRACTION58
3.6397-3.86760.27531250.26622351X-RAY DIFFRACTION79
3.8676-4.1660.29651510.24742816X-RAY DIFFRACTION95
4.166-4.58480.28981580.21712963X-RAY DIFFRACTION99
4.5848-5.24730.31441570.20343006X-RAY DIFFRACTION100
5.2473-6.60750.30721610.24733051X-RAY DIFFRACTION100
6.6075-44.1640.23781670.19663157X-RAY DIFFRACTION99
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)
13.01631.71231.72114.00970.71075.06830.5620.4103-0.9872-1.32510.04161.05042.0127-0.4554-0.5271.3155-0.0501-0.61191.0494-0.02371.2594-33.6399-93.8723-98.2739
23.50832.3121-0.68634.0675-2.21963.88190.89230.82941.0601-0.6587-0.0269-0.6358-1.9570.4296-0.60941.66710.14170.70651.04430.06951.140912.4945-52.5534-98.2997
33.7174-3.54812.79517.0407-4.12545.17910.3589-0.1668-0.6535-0.5254-0.21180.23380.6895-0.0397-0.0820.4064-0.0121-0.01610.44750.03050.5052-5.6268-102.8692-75.3528
42.5081-2.9339-2.4296.70093.96874.36980.2418-0.04050.3775-0.4116-0.1643-0.1532-0.5817-0.1541-0.08550.47660.1351-0.00780.4806-0.01330.4818-15.3309-43.5574-75.3596
55.7887-1.5861-0.11322.8924-1.21593.9166-0.4534-0.8105-0.1028-0.3875-0.38120.0101-1.10250.02430.74311.5078-0.0144-0.05750.93870.04030.5469-10.5504-72.4597-141.857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 775:912 )A775 - 912
2X-RAY DIFFRACTION2( CHAIN B AND RESID 775:913 )B775 - 913
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 564:774 OR RESID 929:1145 ) )A564 - 774
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 564:774 OR RESID 929:1145 ) )A929 - 1145
5X-RAY DIFFRACTION4( CHAIN B AND ( RESID 564:774 OR RESID 929:1145 ) )B564 - 774
6X-RAY DIFFRACTION4( CHAIN B AND ( RESID 564:774 OR RESID 929:1145 ) )B929 - 1145
7X-RAY DIFFRACTION5( CHAIN A AND RESID 529:563 ) OR ( CHAIN B AND RESID 531:563 )A529 - 563
8X-RAY DIFFRACTION5( CHAIN A AND RESID 529:563 ) OR ( CHAIN B AND RESID 531:563 )B531 - 563

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