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- PDB-4m8n: Crystal Structure of PlexinC1/Rap1B Complex -

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Basic information

Entry
Database: PDB / ID: 4m8n
TitleCrystal Structure of PlexinC1/Rap1B Complex
Components
  • PlexinC1 Intracellular Region
  • Ras-related protein Rap-1b
KeywordsSIGNALING PROTEIN / GTPase / GTPase activating protein / Rap / GTP binding / Magnesium Binding / Membrane
Function / homology
Function and homology information


Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / semaphorin receptor activity / Rap1 signalling / establishment of endothelial barrier ...Rap protein signal transduction / modification of postsynaptic structure / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / semaphorin receptor activity / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / cellular response to cAMP / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / small monomeric GTPase / G protein activity / axon guidance / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras-related protein Rap1 / 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 ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras-related protein Rap1 / 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 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rap-1b / Plexin C1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.294 Å
AuthorsPascoe, H.G. / Wang, Y. / Brautigam, C.A. / He, H. / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PlexinC1 Intracellular Region
B: PlexinC1 Intracellular Region
C: PlexinC1 Intracellular Region
D: PlexinC1 Intracellular Region
E: Ras-related protein Rap-1b
F: Ras-related protein Rap-1b
G: Ras-related protein Rap-1b
H: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,71020
Polymers362,5048
Non-polymers2,20612
Water18010
1
A: PlexinC1 Intracellular Region
D: PlexinC1 Intracellular Region
E: Ras-related protein Rap-1b
H: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,35510
Polymers181,2524
Non-polymers1,1036
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-77 kcal/mol
Surface area61100 Å2
MethodPISA
2
B: PlexinC1 Intracellular Region
C: PlexinC1 Intracellular Region
F: Ras-related protein Rap-1b
G: Ras-related protein Rap-1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,35510
Polymers181,2524
Non-polymers1,1036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-75 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.276, 84.734, 138.752
Angle α, β, γ (deg.)91.09, 95.15, 90.32
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
PlexinC1 Intracellular Region


Mass: 69216.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Plexin C1, plxnc1 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Arctic Express) / References: UniProt: Q5RGW1
#2: Protein
Ras-related protein Rap-1b / GTP-binding protein smg p21B


Mass: 21409.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.11, Rap 1B, RAP1B / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61224

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Non-polymers , 4 types, 22 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M HEPES, 5% 2-propanol, 25% PEG 3350, 3.6% polypropylene glycol P400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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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 13, 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: 3.294→50 Å / Num. all: 51910 / Num. obs: 47245 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 106.4 Å2 / Rsym value: 0.052 / Net I/σ(I): 18.6
Reflection shellResolution: 3.294→3.36 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.487 / % possible all: 89.2

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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: 3.294→41.053 Å / SU ML: 0.56 / σ(F): 1.98 / Phase error: 35.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2995 1804 3.82 %
Rwork0.2427 --
obs0.2449 47207 90.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.294→41.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22086 0 132 10 22228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522624
X-RAY DIFFRACTIONf_angle_d0.70230725
X-RAY DIFFRACTIONf_dihedral_angle_d12.6187843
X-RAY DIFFRACTIONf_chiral_restr0.0463663
X-RAY DIFFRACTIONf_plane_restr0.0023885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.294-3.38340.36981270.32183168X-RAY DIFFRACTION81
3.3834-3.48290.35261360.30333418X-RAY DIFFRACTION89
3.4829-3.59520.33661360.28443473X-RAY DIFFRACTION90
3.5952-3.72360.39451380.28723458X-RAY DIFFRACTION89
3.7236-3.87260.34951350.28123399X-RAY DIFFRACTION88
3.8726-4.04870.31111390.26763433X-RAY DIFFRACTION88
4.0487-4.2620.31271350.24843409X-RAY DIFFRACTION88
4.262-4.52870.28941310.2353452X-RAY DIFFRACTION89
4.5287-4.87780.31921370.23273497X-RAY DIFFRACTION91
4.8778-5.36770.31450.22573580X-RAY DIFFRACTION92
5.3677-6.14220.31231450.24833700X-RAY DIFFRACTION96
6.1422-7.73010.27111520.24423772X-RAY DIFFRACTION97
7.7301-41.05630.25661480.21183644X-RAY DIFFRACTION95
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)
17.0163-0.421-1.48139.08891.70177.18280.4839-0.47650.2550.7354-0.0747-1.2733-0.93230.8725-0.40930.8606-0.2159-0.17371.0632-0.00790.76849.8109199.8424-191.2474
27.27430.01461.65163.9946-0.66689.04690.67920.6675-0.0233-0.6967-0.2697-0.95881.07621.4447-0.43320.72810.19610.1640.91940.02331.022148.0493135.0333-132.7445
35.9003-0.19612.6238.2381-0.24372.73920.3873-0.70560.81260.5443-0.53890.5392-0.0123-0.38320.03650.93450.0060.26140.9625-0.01930.769734.9223197.0488-113.7216
48.15211.23030.61327.1421.22167.41680.31710.6833-1.14810.1484-0.3433-0.22540.5051-0.5161-0.03490.76670.0543-0.20590.8103-0.23561.3952-3.1031137.3108-209.9596
56.8693-2.35270.20134.74090.1532.09130.38470.0967-0.6239-0.51110.02361.07910.2321-0.7865-0.39150.7805-0.0438-0.21450.86310.14740.8626-24.4972190.4095-204.2288
67.47471.536-1.26664.69160.27072.37890.0074-0.1484-0.28150.4639-0.25121.4805-0.0441-0.82380.08050.64870.01940.32980.91770.00841.315314.2207144.5564-119.3151
71.60830.26150.02684.0682-1.42826.0972-0.16110.59610.0198-1.2595-0.06160.0061-0.2457-0.15860.24951.3970.06620.05420.7547-0.00660.683335.4674187.9366-150.9294
81.19250.3711-0.22933.039-0.07074.8322-0.1226-0.40960.20871.1704-0.11110.22830.7344-0.12830.2411.62940.0764-0.18260.7594-0.11821.2022-2.4848146.3013-172.4526
93.6436-0.1856-0.78063.1795-2.22955.62960.35061.2972-0.4813-1.24270.20160.2770.50740.5568-0.44351.66750.1868-0.28911.3766-0.21380.8009-13.3472185.0722-224.4652
106.8318-0.76340.33325.9043.3222.3305-0.17440.5555-0.3988-1.01580.0507-1.2349-0.30140.75020.39141.38350.07060.46691.0490.14591.198257.691182.0885-147.5264
114.92920.2568-1.66914.92950.50255.08140.2335-1.95820.50141.8884-0.0910.27130.35220.301-0.0461.364-0.14420.2751.6538-0.1821.02125.2144150.0612-99.5517
123.54680.3907-0.17585.3091-0.10515.9973-0.2766-0.43520.84870.9046-0.0337-2.02240.24791.4610.50461.34860.1585-0.73511.1665-0.05582.217619.7232152.9009-176.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 775:925 )A775 - 925
2X-RAY DIFFRACTION2( CHAIN B AND RESID 775:925 )B775 - 925
3X-RAY DIFFRACTION3( CHAIN C AND RESID 775:913 )C775 - 913
4X-RAY DIFFRACTION4( CHAIN D AND RESID 775:912 )D775 - 912
5X-RAY DIFFRACTION5( CHAIN A AND ( RESID 554:774 OR RESID 926:1146 ) )A554 - 774
6X-RAY DIFFRACTION5( CHAIN A AND ( RESID 554:774 OR RESID 926:1146 ) )A926 - 1146
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 553:774 OR RESID 926:1145 ) )B553 - 774
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 553:774 OR RESID 926:1145 ) )B926 - 1145
9X-RAY DIFFRACTION7( CHAIN C AND ( RESID 558:774 OR RESID 926:1145 ) )C558 - 774
10X-RAY DIFFRACTION7( CHAIN C AND ( RESID 558:774 OR RESID 926:1145 ) )C926 - 1145
11X-RAY DIFFRACTION8( CHAIN D AND ( RESID 558:774 OR RESID 929:1145 ) )D558 - 774
12X-RAY DIFFRACTION8( CHAIN D AND ( RESID 558:774 OR RESID 929:1145 ) )D929 - 1145
13X-RAY DIFFRACTION9( CHAIN E AND ( RESID 1:168 OR RESID 200:202 ) )E1 - 168
14X-RAY DIFFRACTION9( CHAIN E AND ( RESID 1:168 OR RESID 200:202 ) )E200 - 202
15X-RAY DIFFRACTION10( CHAIN F AND ( RESID 2:167 OR RESID 200:202 ) )F2 - 167
16X-RAY DIFFRACTION10( CHAIN F AND ( RESID 2:167 OR RESID 200:202 ) )F200 - 202
17X-RAY DIFFRACTION11( CHAIN G AND ( RESID 1:168 OR RESID 200:202 ) )G1 - 168
18X-RAY DIFFRACTION11( CHAIN G AND ( RESID 1:168 OR RESID 200:202 ) )G200 - 202
19X-RAY DIFFRACTION12( CHAIN H AND ( RESID 1:167 OR RESID 200:202 ) )H1 - 167
20X-RAY DIFFRACTION12( CHAIN H AND ( RESID 1:167 OR RESID 200:202 ) )H200 - 202

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