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- PDB-5b4w: Crystal structure of Plexin inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5b4w
TitleCrystal structure of Plexin inhibitor complex
Components
  • Plexin-B1
  • Synthesized cyclic peptide
KeywordsSIGNALING PROTEIN / Plexin / Inhibitor
Function / homology
Function and homology information


semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / inhibitory synapse assembly / Sema4D mediated inhibition of cell attachment and migration ...semaphorin receptor binding / negative regulation of osteoblast proliferation / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / inhibitory synapse assembly / Sema4D mediated inhibition of cell attachment and migration / positive regulation of axonogenesis / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / semaphorin-plexin signaling pathway / positive regulation of GTPase activity / neuron projection morphogenesis / synapse assembly / regulation of cell migration / GTPase activator activity / transmembrane signaling receptor activity / cell migration / regulation of cell shape / G alpha (12/13) signalling events / postsynaptic membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / glutamatergic synapse / extracellular region / plasma membrane
Similarity search - Function
Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain ...Plexin-B, PSI domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMatsunaga, Y. / Kitago, Y. / Arimori, T. / Takagi, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
AMED Japan
CitationJournal: Cell Chem Biol / Year: 2016
Title: Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide
Authors: Matsunaga, Y. / Bashiruddin, N.K. / Kitago, Y. / Takagi, J. / Suga, H.
History
DepositionApr 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: chem_comp / diffrn_source
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-B1
B: Plexin-B1
C: Plexin-B1
D: Plexin-B1
E: Plexin-B1
F: Plexin-B1
G: Synthesized cyclic peptide
H: Synthesized cyclic peptide
I: Synthesized cyclic peptide
J: Synthesized cyclic peptide
K: Synthesized cyclic peptide
L: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,26619
Polymers383,71712
Non-polymers1,5487
Water86548
1
A: Plexin-B1
G: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1743
Polymers63,9532
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area19560 Å2
MethodPISA
2
B: Plexin-B1
H: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3954
Polymers63,9532
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint0 kcal/mol
Surface area19550 Å2
MethodPISA
3
C: Plexin-B1
I: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1743
Polymers63,9532
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-3 kcal/mol
Surface area20350 Å2
MethodPISA
4
D: Plexin-B1
J: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1743
Polymers63,9532
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-2 kcal/mol
Surface area19820 Å2
MethodPISA
5
E: Plexin-B1
K: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1743
Polymers63,9532
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-3 kcal/mol
Surface area21670 Å2
MethodPISA
6
F: Plexin-B1
L: Synthesized cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1743
Polymers63,9532
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-3 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.426, 217.924, 106.475
Angle α, β, γ (deg.)90.00, 115.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Plexin-B1 / Semaphorin receptor SEP


Mass: 61933.488 Da / Num. of mol.: 6 / Fragment: UNP residues 20-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pcDNA3.1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: O43157
#2: Protein/peptide
Synthesized cyclic peptide


Mass: 2019.380 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThese residues are signal peptide

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 0.1M tri-sodium citrate, 13% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2014 / Details: KB mirror
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 116573 / % possible obs: 97.2 % / Redundancy: 3 % / Biso Wilson estimate: 58.7 Å2 / CC1/2: 0.57 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 1.21 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2341: ???)refinement
DENZOdata collection
SCALEPACKdata scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OL2

3ol2


Resolution: 2.6→40.805 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 5686 5.02 %Random selection
Rwork0.2245 ---
obs0.2266 113157 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→40.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21089 0 98 48 21235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721750
X-RAY DIFFRACTIONf_angle_d1.01429741
X-RAY DIFFRACTIONf_dihedral_angle_d16.29312984
X-RAY DIFFRACTIONf_chiral_restr0.0553327
X-RAY DIFFRACTIONf_plane_restr0.0073933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62960.35611620.32113157X-RAY DIFFRACTION86
2.6296-2.66050.35661860.31043311X-RAY DIFFRACTION90
2.6605-2.69290.3411720.30783373X-RAY DIFFRACTION92
2.6929-2.7270.34771730.29733433X-RAY DIFFRACTION92
2.727-2.76290.37031830.29513448X-RAY DIFFRACTION94
2.7629-2.80070.32751880.29643474X-RAY DIFFRACTION94
2.8007-2.84070.30911840.29523474X-RAY DIFFRACTION95
2.8407-2.88310.32121650.28143582X-RAY DIFFRACTION96
2.8831-2.92820.29721830.2813499X-RAY DIFFRACTION96
2.9282-2.97620.36971950.27423603X-RAY DIFFRACTION97
2.9762-3.02750.30471900.27173553X-RAY DIFFRACTION97
3.0275-3.08250.35881840.27383639X-RAY DIFFRACTION98
3.0825-3.14180.31841710.27213641X-RAY DIFFRACTION98
3.1418-3.20590.32731920.26343614X-RAY DIFFRACTION98
3.2059-3.27550.31841980.24763631X-RAY DIFFRACTION99
3.2755-3.35170.27822020.24673640X-RAY DIFFRACTION99
3.3517-3.43550.28441950.2373670X-RAY DIFFRACTION99
3.4355-3.52830.26021930.22543630X-RAY DIFFRACTION99
3.5283-3.63210.28171880.22173646X-RAY DIFFRACTION99
3.6321-3.74920.26821930.21013649X-RAY DIFFRACTION99
3.7492-3.88310.23551830.21033667X-RAY DIFFRACTION99
3.8831-4.03850.23852110.2113657X-RAY DIFFRACTION99
4.0385-4.22210.24082010.19333671X-RAY DIFFRACTION99
4.2221-4.44440.22821940.17463683X-RAY DIFFRACTION99
4.4444-4.72250.19122050.16953624X-RAY DIFFRACTION99
4.7225-5.08650.19742020.17543710X-RAY DIFFRACTION100
5.0865-5.59720.25471980.19443667X-RAY DIFFRACTION100
5.5972-6.40450.24622090.21783678X-RAY DIFFRACTION100
6.4045-8.05880.26841970.21193712X-RAY DIFFRACTION100
8.0588-40.810.24591890.22213735X-RAY DIFFRACTION100
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)
10.7627-0.26080.16210.4060.18011.7797-0.0104-0.2233-0.02010.15750.0359-0.01530.0973-0.0836-0.0920.31520.0754-0.03810.4514-0.01430.3338108.6351-37.72181.4437
20.7567-0.01690.43850.7246-0.11051.81750.02960.0121-0.0840.0148-0.00380.01650.0952-0.1075-0.09560.21710.0643-0.04370.3541-0.0320.367395.2681-35.1234.9478
31.51410.0015-0.28130.78120.15081.8860.12710.1590.0337-0.0235-0.1071-0.0104-0.2518-0.0639-0.08670.4383-0.01240.11690.23780.01150.316679.48654.098128.2936
41.0471-0.2217-0.63840.84710.2561.93790.0256-0.0829-0.11030.1626-0.06460.1284-0.3114-0.6365-0.06370.58130.08590.18190.61650.01250.380751.74325.337167.7011
50.82850.11540.66690.76520.00431.64710.1043-0.0279-0.03670.23150.0954-0.09380.36060.3058-0.08540.44330.1171-0.08350.3952-0.11250.4123142.5361-61.403247.905
60.77330.26190.08891.4213-0.65261.08980.19030.06120.46330.0578-0.2406-0.0196-0.47510.4355-0.09980.4531-0.17060.07840.639-0.06780.6601148.3117-30.505126.1891
70.6161-0.36640.25850.8250.33691.92450.2210.2689-0.212-0.2185-0.08790.19030.43980.0911-0.02260.65710.1184-0.18310.3511-0.14590.4778121.5588-70.144.9775
81.3237-0.49640.16721.13610.90861.0392-0.10740.1548-0.1407-0.26630.08650.3296-0.0563-0.0136-0.1010.31870.1219-0.04110.65990.01910.428987.8347-36.656564.6973
90.4924-0.49540.34570.97520.00050.49230.07380.0710.16620.29120.124-0.2922-0.10040.3673-0.1140.3620.098-0.03590.5228-0.08150.4205113.6183-27.550152.8947
101.1202-0.07640.10241.3299-0.16751.2407-0.1019-0.2452-0.18330.46050.133-0.0135-0.2319-0.0507-0.09010.4587-0.02920.10030.3182-0.02440.382679.73785.901555.0235
111.4241-0.24230.3121.37230.23211.34710.05370.354-0.0298-0.31180.1482-0.0078-0.3534-0.529-0.09060.65470.17250.15530.76320.01460.386953.726811.69541.969
121.5161-0.11260.08730.9316-0.32751.08410.1050.4340.0863-0.0705-0.06170.0416-0.05450.0838-0.0730.3704-0.0175-0.00760.3977-0.0890.3157135.8777-50.973224.1341
131.2419-0.4734-0.66030.60380.1371.17510.0092-0.0873-0.31790.11390.2098-0.02170.36470.3541-0.12150.80280.2266-0.17960.3647-0.20550.5794136.1798-80.753424.7975
148.7751-2.17974.92745.3453-0.44873.4925-0.45580.2561.58190.57130.1436-1.13480.07860.05760.3370.8315-0.0497-0.11320.67150.12050.6119106.027-53.109264.3387
150.6388-0.54740.31031.1703-0.81031.42670.13680.1811-0.0266-0.06590.0003-0.01050.0557-0.0095-0.09570.4880.0209-0.20880.68430.00750.6999101.7429-31.842929.7109
164.86463.21944.41552.57742.80914.0364-0.2992-0.24310.2557-0.56610.03790.0408-0.8412-0.65870.33450.69270.0680.04830.55150.06640.630670.0995-12.186541.8394
178.7996.29694.30542220.60320.65580.87830.4487-1.8965-1.15430.42021.4151.31580.7140.01030.32011.0303-0.14640.986855.8137-10.880251.5652
184.5123.0545-3.48883.4351-1.59362-0.4384-0.4913-0.5759-1.0161-0.311-0.58461.55890.42040.73170.71690.1439-0.1220.50220.05020.6232120.7557-61.502940.6748
195.9343-3.83715.21944.2995-0.51699.08190.00240.30320.40920.0155-0.1497-0.45490.2319-0.06670.17030.848-0.1017-0.33750.4496-0.04640.6902114.2575-69.898727.1401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:481 )A26 - 481
2X-RAY DIFFRACTION2( CHAIN B AND RESID 26:481 )B26 - 481
3X-RAY DIFFRACTION3( CHAIN C AND RESID 26:481 )C26 - 481
4X-RAY DIFFRACTION4( CHAIN D AND RESID 24:481 )D24 - 481
5X-RAY DIFFRACTION5( CHAIN E AND RESID 26:482 )E26 - 482
6X-RAY DIFFRACTION6( CHAIN E AND RESID 483:528 )E483 - 528
7X-RAY DIFFRACTION7( CHAIN F AND RESID 26:481 )F26 - 481
8X-RAY DIFFRACTION8( CHAIN G AND ( RESID 0:16 OR RESID 17:17 ) )G0 - 16
9X-RAY DIFFRACTION8( CHAIN G AND ( RESID 0:16 OR RESID 17:17 ) )G17
10X-RAY DIFFRACTION9( CHAIN H AND ( RESID 0:16 OR RESID 17:17 ) )H0 - 16
11X-RAY DIFFRACTION9( CHAIN H AND ( RESID 0:16 OR RESID 17:17 ) )H17
12X-RAY DIFFRACTION10( CHAIN I AND ( RESID 0:16 OR RESID 17:17 ) )I0 - 16
13X-RAY DIFFRACTION10( CHAIN I AND ( RESID 0:16 OR RESID 17:17 ) )I17
14X-RAY DIFFRACTION11( CHAIN J AND ( RESID 0:16 OR RESID 17:17 ) )J0 - 16
15X-RAY DIFFRACTION11( CHAIN J AND ( RESID 0:16 OR RESID 17:17 ) )J17
16X-RAY DIFFRACTION12( CHAIN K AND ( RESID 0:16 OR RESID 17:17 ) )K0 - 16
17X-RAY DIFFRACTION12( CHAIN K AND ( RESID 0:16 OR RESID 17:17 ) )K17
18X-RAY DIFFRACTION13( CHAIN L AND ( RESID 0:16 OR RESID 17:17 ) )L0 - 16
19X-RAY DIFFRACTION13( CHAIN L AND ( RESID 0:16 OR RESID 17:17 ) )L17
20X-RAY DIFFRACTION14( CHAIN A AND RESID 601:601 )A601
21X-RAY DIFFRACTION15( CHAIN B AND RESID 601:602 )B601 - 602
22X-RAY DIFFRACTION16( CHAIN C AND RESID 601:601 )C601
23X-RAY DIFFRACTION17( CHAIN D AND RESID 601:601 )D601
24X-RAY DIFFRACTION18( CHAIN E AND RESID 601:601 )E601
25X-RAY DIFFRACTION19( CHAIN F AND RESID 601:601 )F601

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