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- PDB-4nxr: Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PD... -

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Basic information

Entry
Database: PDB / ID: 4nxr
TitleCrystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Neurexin-1 Peptide
Components
  • Neurexin-2-beta Peptide
  • T-lymphoma invasion and metastasis-inducing protein 1
Keywordssignaling Protein/Peptide / Beta barrel fold protein / PDZ domain / peptide binding / specificity mutant / scaffold signaling protein for cell adhesion and cell junction / signaling domain / signaling Protein-Peptide complex
Function / homology
Function and homology information


positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / neuroligin family protein binding / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus ...positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / neuroligin family protein binding / Activated NTRK2 signals through CDK5 / neuron cell-cell adhesion / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / Neurexins and neuroligins / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / main axon / neuron projection extension / small GTPase-mediated signal transduction / positive regulation of axonogenesis / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / axonal growth cone / RAC1 GTPase cycle / EPHB-mediated forward signaling / cell adhesion molecule binding / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / response to cocaine / receptor tyrosine kinase binding / ruffle membrane / kinase binding / G alpha (12/13) signalling events / cell-cell junction / cell migration / transmembrane signaling receptor activity / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / membrane => GO:0016020 / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / signal transduction / plasma membrane / cytosol
Similarity search - Function
TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Laminin G domain profile. / Laminin G domain / Laminin G domain / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PDZ domain / Pdz3 Domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Concanavalin A-like lectin/glucanase domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-ANS / Neurexin-2-beta / Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, X. / Speckhard, D.C. / Shepherd, T.R. / Hengel, S.R. / Fuentes, E.J.
CitationJournal: Structure / Year: 2016
Title: Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.
Authors: Liu, X. / Speckhard, D.C. / Shepherd, T.R. / Sun, Y.J. / Hengel, S.R. / Yu, L. / Fowler, C.A. / Gakhar, L. / Fuentes, E.J.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-lymphoma invasion and metastasis-inducing protein 1
B: Neurexin-2-beta Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7424
Polymers11,2532
Non-polymers4902
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-0 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.358, 50.323, 61.942
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 T-lymphoma invasion and metastasis-inducing protein 1 / TIAM-1


Mass: 10192.402 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: L911M, K912E, L915F, L920V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: TIAM1 / Plasmid: PET21A-6HIS-rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13009
#2: Protein/peptide Neurexin-2-beta Peptide / Neurexin II-beta Peptide


Mass: 1060.158 Da / Num. of mol.: 1 / Fragment: UNP residue 659-666 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P58401
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ANS / 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID) / DANSYL ACID


Mass: 251.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Sodium acetate, 0.1M HEPES, pH=7.5, 22% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 14, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39.06 Å / Num. obs: 6821 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 39.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.035 / Mean I/σ(I) obs: 11 / % possible all: 87.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KZD

3kzd


Resolution: 1.9→39.06 Å / SU ML: 0.15 / σ(F): 0.64 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 311 4.56 %
Rwork0.1466 --
obs0.1489 6821 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 31 99 919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008832
X-RAY DIFFRACTIONf_angle_d1.1571118
X-RAY DIFFRACTIONf_dihedral_angle_d14.309312
X-RAY DIFFRACTIONf_chiral_restr0.045120
X-RAY DIFFRACTIONf_plane_restr0.005142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.09120.23341240.15372881X-RAY DIFFRACTION96
2.0912-2.39380.24271510.15322998X-RAY DIFFRACTION100
2.3938-3.01570.22481400.1632953X-RAY DIFFRACTION100
3.0157-39.06610.14591500.1322981X-RAY DIFFRACTION100

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