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

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Basic information

Entry
Database: PDB / ID: 4nxq
TitleCrystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM) in Complex With Caspr4 Peptide
Components
  • Contactin-associated protein-like 4 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 / protein-peptide complex / 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 / regulation of synaptic transmission, dopaminergic / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of grooming behavior / 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 / regulation of synaptic transmission, dopaminergic / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of grooming behavior / 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 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / main axon / neuron projection extension / regulation of synaptic transmission, GABAergic / 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 / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / response to cocaine / cell projection / receptor tyrosine kinase binding / ruffle membrane / kinase binding / G alpha (12/13) signalling events / cell-cell junction / cell migration / presynaptic membrane / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / membrane => GO:0016020 / cell adhesion / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / plasma membrane / cytosol
Similarity search - Function
Contactin-associated protein-like 4 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / 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 ...Contactin-associated protein-like 4 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / 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 / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal 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 / Epidermal growth factor-like domain. / PH domain / EGF-like domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / EGF-like domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM1 / Contactin-associated protein-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: T-lymphoma invasion and metastasis-inducing protein 1
C: T-lymphoma invasion and metastasis-inducing protein 1
D: Contactin-associated protein-like 4 peptide
E: Contactin-associated protein-like 4 peptide
F: Contactin-associated protein-like 4 peptide


Theoretical massNumber of molelcules
Total (without water)33,8936
Polymers33,8936
Non-polymers00
Water2,882160
1
A: T-lymphoma invasion and metastasis-inducing protein 1
D: Contactin-associated protein-like 4 peptide


Theoretical massNumber of molelcules
Total (without water)11,2982
Polymers11,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area5790 Å2
MethodPISA
2
B: T-lymphoma invasion and metastasis-inducing protein 1
E: Contactin-associated protein-like 4 peptide


Theoretical massNumber of molelcules
Total (without water)11,2982
Polymers11,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area6070 Å2
MethodPISA
3
C: T-lymphoma invasion and metastasis-inducing protein 1
F: Contactin-associated protein-like 4 peptide


Theoretical massNumber of molelcules
Total (without water)11,2982
Polymers11,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.078, 50.817, 53.036
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein T-lymphoma invasion and metastasis-inducing protein 1 / TIAM-1


Mass: 10192.402 Da / Num. of mol.: 3 / 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 Contactin-associated protein-like 4 peptide / Caspr4 peptide


Mass: 1105.176 Da / Num. of mol.: 3 / Fragment: UNP residues 1301-1308 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9C0A0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Magnesium chloride, 0.1M MES, pH=6.5, 20% 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 18, 2010
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: 2.1→37.52 Å / Num. all: 16019 / Num. obs: 15923 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 22.85 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2334 / % possible all: 100

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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: 2.1→37.52 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 793 4.99 %RANDOM
Rwork0.1851 ---
obs0.1876 15904 99.24 %-
all-16026 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 0 160 2438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082313
X-RAY DIFFRACTIONf_angle_d1.1663114
X-RAY DIFFRACTIONf_dihedral_angle_d12.5843
X-RAY DIFFRACTIONf_chiral_restr0.052349
X-RAY DIFFRACTIONf_plane_restr0.006406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23160.30691120.21062517X-RAY DIFFRACTION100
2.2316-2.40380.27191450.21182512X-RAY DIFFRACTION100
2.4038-2.64570.27211290.21392509X-RAY DIFFRACTION99
2.6457-3.02840.25511410.20642513X-RAY DIFFRACTION100
3.0284-3.81480.2281420.1732508X-RAY DIFFRACTION99
3.8148-37.520.19121240.15942552X-RAY DIFFRACTION98

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