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- PDB-3axa: Crystal structure of afadin PDZ domain in complex with the C-term... -

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Basic information

Entry
Database: PDB / ID: 3axa
TitleCrystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3
ComponentsAfadin, Nectin-3
KeywordsCELL ADHESION / PDZ domain / AF-6 / fusion protein
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / retina morphogenesis in camera-type eye / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / pore complex assembly / Adherens junctions interactions ...Nectin/Necl trans heterodimerization / retina morphogenesis in camera-type eye / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / adherens junction maintenance / establishment of protein localization to plasma membrane / regulation of postsynapse assembly / protein localization to cell junction / pore complex assembly / Adherens junctions interactions / dendrite arborization / lens morphogenesis in camera-type eye / LIM domain binding / telencephalon development / neuroepithelial cell differentiation / cell-cell adhesion mediated by cadherin / positive regulation of dendritic spine morphogenesis / positive regulation of dendrite extension / cell-cell contact zone / brain morphogenesis / fertilization / positive regulation of mini excitatory postsynaptic potential / positive regulation of dendrite morphogenesis / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / pore complex / homophilic cell adhesion via plasma membrane adhesion molecules / homeostasis of number of cells / presynaptic active zone membrane / cell adhesion molecule binding / somatodendritic compartment / hippocampal mossy fiber to CA3 synapse / adherens junction / postsynaptic density membrane / cerebral cortex development / cell-cell adhesion / regulation of protein localization / cell-cell junction / cell junction / apical part of cell / cell adhesion / symbiont entry into host cell / axon / dendrite / signal transduction / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Nectin-3 / Nectin-4 / : / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. ...Nectin-3 / Nectin-4 / : / Afadin, cargo binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ubiquitin-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsFujiwara, Y. / Goda, N. / Narita, H. / Satomura, K. / Nakagawa, A. / Sakisaka, T. / Suzuki, M. / Hiroaki, H.
CitationJournal: Protein Sci. / Year: 2015
Title: Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site.
Authors: Fujiwara, Y. / Goda, N. / Tamashiro, T. / Narita, H. / Satomura, K. / Tenno, T. / Nakagawa, A. / Oda, M. / Suzuki, M. / Sakisaka, T. / Takai, Y. / Hiroaki, H.
History
DepositionMar 31, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Afadin, Nectin-3
B: Afadin, Nectin-3


Theoretical massNumber of molelcules
Total (without water)22,2092
Polymers22,2092
Non-polymers00
Water21612
1
A: Afadin, Nectin-3

A: Afadin, Nectin-3


Theoretical massNumber of molelcules
Total (without water)22,2092
Polymers22,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area10590 Å2
MethodPISA
2
B: Afadin, Nectin-3

B: Afadin, Nectin-3


Theoretical massNumber of molelcules
Total (without water)22,2092
Polymers22,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.477, 90.481, 88.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 1 - 97 / Label seq-ID: 10 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Afadin, Nectin-3 / Protein Af-6


Mass: 11104.712 Da / Num. of mol.: 2
Fragment: PDZ domain (UNP 1003-1095), C-terminal peptide (UNP 544-549)
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Afadin (1003-1095) and Nectin-3 (544-549)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mllt4, Af6 / Plasmid: pGEX-6P3-PRESAT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QZQ1, UniProt: Q9JLB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. all: 5641 / Num. obs: 5357 / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.5
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.246 / Num. unique all: 255 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FE5

2fe5


Resolution: 2.78→47.29 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 37.465 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26336 255 4.5 %RANDOM
Rwork0.24032 ---
obs0.24133 5357 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.671 Å2
Baniso -1Baniso -2Baniso -3
1-6.75 Å20 Å20 Å2
2---1.88 Å20 Å2
3----4.87 Å2
Refinement stepCycle: LAST / Resolution: 2.78→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 0 12 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221434
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9831928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8472450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2591512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1551.5948
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22621504
X-RAY DIFFRACTIONr_scbond_it2.4963486
X-RAY DIFFRACTIONr_scangle_it4.6994.5424
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 713 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.060.5
LS refinement shellResolution: 2.778→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 15 -
Rwork0.335 275 -
obs--68.88 %
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)
12.34240.89380.43641.0911-0.99613.1389-0.0413-0.2094-0.0289-0.0929-0.0297-0.02470.6190.59370.0710.41560.23820.00550.40780.03540.223135.6578-12.258130.4247
20.17770.31880.87692.35380.96185.7369-0.0065-0.1444-0.0444-0.2341-0.1756-0.1274-0.9508-1.03850.1820.54310.2885-0.07140.3407-0.00940.208415.24848.061736.1789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 97
2X-RAY DIFFRACTION2B1 - 97

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