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- PDB-3nvq: Molecular mechanism of guidance cue recognition -

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Basic information

Entry
Database: PDB / ID: 3nvq
TitleMolecular mechanism of guidance cue recognition
Components
  • Plexin-C1
  • Semaphorin-7A
KeywordsSIGNALING PROTEIN/protein binding / Beta-Propeller / signaling / SIGNALING PROTEIN-protein binding complex
Function / homology
Function and homology information


olfactory lobe development / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / chemorepellent activity / negative regulation of cell adhesion / positive regulation of macrophage cytokine production ...olfactory lobe development / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / chemorepellent activity / negative regulation of cell adhesion / positive regulation of macrophage cytokine production / neural crest cell migration / negative chemotaxis / semaphorin-plexin signaling pathway / positive regulation of axonogenesis / positive regulation of axon extension / axon extension / regulation of GTPase activity / regulation of cell migration / : / integrin-mediated signaling pathway / axon guidance / osteoblast differentiation / integrin binding / regulation of inflammatory response / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of cell migration / cell adhesion / inflammatory response / external side of plasma membrane / signaling receptor binding / plasma membrane => GO:0005886 / extracellular space / membrane / plasma membrane
Similarity search - Function
Semaphorin-7A, sema domain / Plexin-C1, Sema domain / Semaphorin / Plexin cytoplasmic RasGAP domain / Plexin, cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin family / Plexin repeat / Plexin repeat ...Semaphorin-7A, sema domain / Plexin-C1, Sema domain / Semaphorin / Plexin cytoplasmic RasGAP domain / Plexin, cytoplasmic RasGAP 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 profile. / Sema domain superfamily / IPT/TIG domain / Immunoglobulin domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Methylamine Dehydrogenase; Chain H / 7 Propeller / WD40/YVTN repeat-like-containing domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Plexin-C1 / Semaphorin-7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsJuo, Z. / Liu, H. / Shim, A. / Focia, P. / Chen, X. / Garcia, C. / He, X.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1.
Authors: Liu, H. / Juo, Z.S. / Shim, A.H. / Focia, P.J. / Chen, X. / Garcia, K.C. / He, X.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-7A
B: Plexin-C1
E: Semaphorin-7A
F: Plexin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,65126
Polymers237,7844
Non-polymers4,86722
Water15,457858
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.645, 126.078, 236.419
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 Semaphorin-7A / Semaphorin-L / Sema L / Semaphorin-K1 / Sema K1 / John-Milton-Hargen human blood group Ag / JMH ...Semaphorin-L / Sema L / Semaphorin-K1 / Sema K1 / John-Milton-Hargen human blood group Ag / JMH blood group antigen / CDw108


Mass: 67092.133 Da / Num. of mol.: 2 / Fragment: UNP residues 45-637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEMA7A, CD108, SEMAL / Cell (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: O75326
#2: Protein Plexin-C1 / Virus-encoded semaphorin protein receptor


Mass: 51800.102 Da / Num. of mol.: 2 / Fragment: UNP residues 33-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNC1, VESPR / Cell (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: O60486
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
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: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG1000, 0.1M Tris pH7.5, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 116579 / Num. obs: 114947 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 29.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5000 / % possible all: 86.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementResolution: 2.4→25.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 113764.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 5694 5 %RANDOM
Rwork0.248 ---
obs0.248 112953 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.21 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 66.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.67 Å20 Å20 Å2
2---0.52 Å20 Å2
3---4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16658 0 308 858 17824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 858 5.1 %
Rwork0.357 15869 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param

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