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- PDB-4cnm: Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1... -

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Basic information

Entry
Database: PDB / ID: 4cnm
TitleCrystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein)
ComponentsTROPHOBLAST GLYCOPROTEIN
KeywordsCELL ADHESION / WAIF1 / TPBG / TROVAX / MVA-5T4 / CANCER / SIGNALING / LEUCINE-RICH REPEATS / WNT/BETA-CATENIN SIGNALING PATHWAY
Function / homology
Function and homology information


mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / positive regulation of synapse assembly / synaptic transmission, GABAergic / axon terminus / protein localization to plasma membrane / cell chemotaxis / negative regulation of canonical Wnt signaling pathway ...mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / positive regulation of synapse assembly / synaptic transmission, GABAergic / axon terminus / protein localization to plasma membrane / cell chemotaxis / negative regulation of canonical Wnt signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / negative regulation of cell population proliferation / dendrite / cell surface / endoplasmic reticulum / plasma membrane
Similarity search - Function
: / Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe ...: / Leucine rich repeat C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Trophoblast glycoprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y.
CitationJournal: Structure / Year: 2014
Title: Structural Insights Into the Inhibition of Wnt Signaling by Cancer Antigen 5T4/Wnt-Activated Inhibitory Factor 1.
Authors: Zhao, Y. / Malinauskas, T. / Harlos, K. / Jones, E.Y.
History
DepositionJan 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TROPHOBLAST GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,93212
Polymers32,9001
Non-polymers2,03211
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.310, 67.310, 96.380
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 , 1 types, 1 molecules A

#1: Protein TROPHOBLAST GLYCOPROTEIN / 5T4 ONCOFETAL ANTIGEN / WNT-ACTIVATED INHIBITORY FACTOR / 5T4 ONCOFETAL TROPHOBLAST GLYCOPROTEIN / ...5T4 ONCOFETAL ANTIGEN / WNT-ACTIVATED INHIBITORY FACTOR / 5T4 ONCOFETAL TROPHOBLAST GLYCOPROTEIN / 5T4 ONCOTROPHOBLAST GLYCOPROTEIN / M6P1


Mass: 32900.395 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PURD-5T4/WAIF1ECTO / Cell line (production host): HEK293S GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: Q13641

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Sugars , 2 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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Non-polymers , 3 types, 130 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growDetails: THE CRYSTALLIZATION DROP CONTAINED 100 NL OF CONCENTRATED 5T4 (5.5 MG/ML), 100 NL OF 25% W/V POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M CITRATE PH 3.5, AND 0.5 NL OF 0.1 M NAOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.06
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.75→49.31 Å / Num. obs: 33062 / % possible obs: 99.8 % / Observed criterion σ(I): 3.1 / Redundancy: 9.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZYJ

3zyj


Resolution: 1.75→43.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.141 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22153 1674 5.1 %RANDOM
Rwork0.18172 ---
obs0.18365 31330 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.524 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--3.22 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 130 124 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192422
X-RAY DIFFRACTIONr_bond_other_d0.0020.022322
X-RAY DIFFRACTIONr_angle_refined_deg1.8332.033298
X-RAY DIFFRACTIONr_angle_other_deg0.9293.0035298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.223.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1661520
X-RAY DIFFRACTIONr_chiral_restr0.1090.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
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_it1.9432.061152
X-RAY DIFFRACTIONr_mcbond_other1.9422.0591151
X-RAY DIFFRACTIONr_mcangle_it2.8143.0751444
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6562.8561270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 117 -
Rwork0.279 2247 -
obs--99.29 %
Refinement TLS params.Method: refined / Origin x: 22.7534 Å / Origin y: -1.2691 Å / Origin z: -12.0136 Å
111213212223313233
T0.0833 Å2-0.0026 Å2-0.0007 Å2-0.0255 Å20.0066 Å2--0.0719 Å2
L1.4734 °2-0.3226 °20.1884 °2-0.1783 °2-0.0551 °2--1.4536 °2
S-0.0389 Å °-0.0897 Å °-0.0024 Å °-0.0045 Å °0.0091 Å °-0.0277 Å °0.0394 Å °-0.1719 Å °0.0298 Å °

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