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

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Basic information

Entry
Database: PDB / ID: 4cnc
TitleCrystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast glycoprotein)
ComponentsTROPHOBLAST GLYCOPROTEIN
KeywordsCELL ADHESION / WAIF1 / TPBG / TROVAX / 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 / synaptic transmission, GABAergic / positive regulation of synapse assembly / axon terminus / cell chemotaxis / protein localization to plasma membrane / negative regulation of canonical Wnt signaling pathway ...mesenchymal cell migration / dendrite arborization / olfactory learning / positive regulation of chemotaxis / synaptic transmission, GABAergic / positive regulation of synapse assembly / axon terminus / cell chemotaxis / protein localization to plasma membrane / negative regulation of canonical Wnt signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / 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 ...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
DI(HYDROXYETHYL)ETHER / Trophoblast glycoprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 21, 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 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TROPHOBLAST GLYCOPROTEIN
B: TROPHOBLAST GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,04532
Polymers65,8012
Non-polymers4,24530
Water3,225179
1
A: TROPHOBLAST GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17616
Polymers32,9001
Non-polymers2,27615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TROPHOBLAST GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,86916
Polymers32,9001
Non-polymers1,96915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 95.820, 65.970
Angle α, β, γ (deg.)90.00, 91.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0099, -0.0092), (0.0106, -0.9974, -0.0712), (-0.0085, -0.0713, 0.9974)
Vector: 24.0785, 21.8856, 34.1235)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32900.395 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 60-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EMBRYONIC KIDNEY / Organ: KIDNEY / 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, 8 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.: 2
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 , 5 types, 201 molecules

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


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.8 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: THE CRYSTALLIZATION SITTING DROP CONTAINED 100 NL OF CONCENTRATED 5T4/WAIF1 (5 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 150 MM NACL) PLUS 100 NL OF 0.2 M (NH4)2SO4, 30 % W/V PEG 4000.

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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: 1.77→54.33 Å / Num. obs: 59830 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T4, CRYSTAL FORM WITH 1 MOLECULE IN THE ASYMMETRIC UNIT

Resolution: 1.77→54.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.104 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21727 3022 5.1 %RANDOM
Rwork0.17725 ---
obs0.17929 56784 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.234 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20.03 Å2
2---0.77 Å20 Å2
3---1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.77→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 257 179 4704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194615
X-RAY DIFFRACTIONr_bond_other_d0.0010.024413
X-RAY DIFFRACTIONr_angle_refined_deg1.9052.0376294
X-RAY DIFFRACTIONr_angle_other_deg0.9173.00310062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63223.846195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5331535
X-RAY DIFFRACTIONr_chiral_restr0.1060.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
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_it1.8382.0742208
X-RAY DIFFRACTIONr_mcbond_other1.8292.0732207
X-RAY DIFFRACTIONr_mcangle_it2.6943.0992753
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5972.8152407
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: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 230 -
Rwork0.245 4125 -
obs--99.52 %
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)
11.2509-0.6994-0.23571.6120.17830.3831-0.0287-0.0649-0.03880.04090.01380.1957-0.00040.01590.01490.0525-0.00530.00380.035-0.00270.026110.3101-0.773831.0497
21.0624-0.34040.04370.97210.09130.2682-0.0132-0.09650.01340.0020.0023-0.0904-0.00140.00030.01090.02690.00770.0010.06170.01680.014513.761322.8682-1.7139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 344
2X-RAY DIFFRACTION2B60 - 344

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