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

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Basic information

Entry
Database: PDB / ID: 4gvc
TitleCrystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide
Components
  • Syndecan-1Syndecan 1
  • T-lymphoma invasion and metastasis-inducing protein 1
KeywordsSIGNALING PROTEIN / phosphorylation / peptide conformational change / new binding pocket / scaffold signaling protein for cell adhesion and cell junction / syndecan1 P1 Tyr phosphorylation / sydencan1 N-terminal Thr dansylation
Function / homology
Function and homology information


myoblast development / positive regulation of Schwann cell chemotaxis / striated muscle cell development / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS ...myoblast development / positive regulation of Schwann cell chemotaxis / striated muscle cell development / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / extrinsic component of postsynaptic density membrane / HS-GAG biosynthesis / HS-GAG degradation / positive regulation of extracellular exosome assembly / Activated NTRK2 signals through CDK5 / Sertoli cell development / 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 / positive regulation of exosomal secretion / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / cargo receptor activity / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / ureteric bud development / main axon / neuron projection extension / Syndecan interactions / small GTPase-mediated signal transduction / positive regulation of axonogenesis / Other interleukin signaling / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / Retinoid metabolism and transport / axonal growth cone / response to glucocorticoid / response to cAMP / RAC1 GTPase cycle / EPHB-mediated forward signaling / receptor-mediated endocytosis / lysosomal lumen / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / response to cocaine / Cell surface interactions at the vascular wall / response to hydrogen peroxide / receptor tyrosine kinase binding / response to toxic substance / ruffle membrane / kinase binding / Golgi lumen / response to calcium ion / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / Attachment and Entry / positive regulation of cell migration / external side of plasma membrane / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / cell surface / protein-containing complex / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Syndecan / Syndecan, conserved site / Syndecans 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 ...Syndecan / Syndecan, conserved site / Syndecans 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 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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 / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-ANS / Syndecan-1 / Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLiu, X. / Shepherd, T.R. / Murray, A.M. / Xu, Z. / Fuentes, E.J.
CitationJournal: Structure / Year: 2013
Title: The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics.
Authors: Liu, X. / Shepherd, T.R. / Murray, A.M. / Xu, Z. / Fuentes, E.J.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: Syndecan-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5966
Polymers11,2512
Non-polymers3454
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-32 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.717, 50.135, 57.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 10154.440 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 841-930)
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 Syndecan-1 / Syndecan 1 / SYND1


Mass: 1096.060 Da / Num. of mol.: 1 / Fragment: UNP residues 303-310 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18827

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Non-polymers , 4 types, 100 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsQ844H IS A NATURAL VARIANT.

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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: 1.72 Å3/Da / Density % sol: 28.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M sodium acetate, 25% PEG4000, 8% isopropanol, 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: Apr 30, 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: 1.54→37.85 Å / Num. all: 11979 / Num. obs: 11440 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.4
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 9.3 / Num. unique all: 1685 / % possible all: 74.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KZD

3kzd


Resolution: 1.54→37.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.964 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19964 546 4.8 %RANDOM
Rwork0.16551 ---
all0.16717 10862 --
obs0.16717 10862 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.54→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 19 96 902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022810
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2652.0131091
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6932534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.547154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02593
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_it0.921.5506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6462802
X-RAY DIFFRACTIONr_scbond_it2.6483304
X-RAY DIFFRACTIONr_scangle_it4.1744.5289
X-RAY DIFFRACTIONr_rigid_bond_restr1.1113804
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 35 -
Rwork0.163 497 -
obs-532 60.73 %

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