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- PDB-4cdj: Structure of ZNRF3 ectodomain -

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Basic information

Entry
Database: PDB / ID: 4cdj
TitleStructure of ZNRF3 ectodomain
ComponentsE3 UBIQUITIN-PROTEIN LIGASE ZNRF3
KeywordsLIGASE / WNT SIGNALING / ADULT STEM CELLS / E3 LIGASE / PROTEASE-ASSOCIATED DOMAIN / ZINC RING FINGER / LGR5 / R-SPONDIN
Function / homology
Function and homology information


regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / stem cell proliferation / RING-type E3 ubiquitin transferase ...regulation of Wnt signaling pathway, planar cell polarity pathway / Wnt receptor catabolic process / negative regulation of non-canonical Wnt signaling pathway / Regulation of FZD by ubiquitination / frizzled binding / regulation of canonical Wnt signaling pathway / limb development / negative regulation of Wnt signaling pathway / stem cell proliferation / RING-type E3 ubiquitin transferase / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / metal ion binding / plasma membrane
Similarity search - Function
E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / Ring finger domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Ring finger / Zinc finger RING-type profile. / 3-Layer(bba) Sandwich / Zinc finger, RING-type ...E3 ubiquitin-protein ligase ZNRF3, Zinc finger, RING-type / ZNRF-3, ectodomain / ZNRF-3 Ectodomain / Ring finger domain / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Ring finger / Zinc finger RING-type profile. / 3-Layer(bba) Sandwich / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / E3 ubiquitin-protein ligase ZNRF3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsPeng, W.C. / de Lau, W. / Madoori, P.K. / Forneris, F. / Granneman, J.C.M. / Clevers, H. / Gros, P.
CitationJournal: Plos One / Year: 2013
Title: Structures of Wnt-Antagonist Znrf3 and its Complex with R-Spondin 1 and Implications for Signaling.
Authors: Peng, W.C. / De Lau, W. / Madoori, P.K. / Forneris, F. / Granneman, J.C.M. / Clevers, H. / Gros, P.
History
DepositionNov 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Atomic model / Derived calculations
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
B: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3298
Polymers35,9732
Non-polymers3566
Water5,332296
1
A: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2195
Polymers17,9861
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1103
Polymers17,9861
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.686, 73.503, 58.573
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 / ZINC/RING FINGER PROTEIN 3


Mass: 17986.316 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 53-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
References: UniProt: Q5SSZ7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGS AT THE N-TERMINUS AND AAAHHHHHH AT C-TERMINUS ARE INTRODUCED BY CLONING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM FORMATE AT PH 6.6 WITH 20% W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→45.57 Å / Num. obs: 46197 / % possible obs: 96.6 % / Observed criterion σ(I): 4.1 / Redundancy: 2.7 % / Biso Wilson estimate: 17.66 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→45.567 Å / SU ML: 0.14 / σ(F): 1.37 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1773 2334 5.1 %
Rwork0.1616 --
obs0.1625 46172 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 23 296 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182501
X-RAY DIFFRACTIONf_angle_d1.8423384
X-RAY DIFFRACTIONf_dihedral_angle_d15.127971
X-RAY DIFFRACTIONf_chiral_restr0.111382
X-RAY DIFFRACTIONf_plane_restr0.01446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.53070.2641310.23782501X-RAY DIFFRACTION93
1.5307-1.5640.24741630.22012465X-RAY DIFFRACTION94
1.564-1.60030.23891470.2032491X-RAY DIFFRACTION94
1.6003-1.64040.21451410.18672539X-RAY DIFFRACTION95
1.6404-1.68470.21141340.17762545X-RAY DIFFRACTION95
1.6847-1.73430.19691380.16552516X-RAY DIFFRACTION95
1.7343-1.79030.22131310.1722574X-RAY DIFFRACTION96
1.7903-1.85430.21051180.1722599X-RAY DIFFRACTION97
1.8543-1.92850.22551150.16252573X-RAY DIFFRACTION96
1.9285-2.01630.1791290.14922601X-RAY DIFFRACTION96
2.0163-2.12260.17211290.15312602X-RAY DIFFRACTION98
2.1226-2.25560.1691760.14852584X-RAY DIFFRACTION97
2.2556-2.42970.16571290.14582625X-RAY DIFFRACTION98
2.4297-2.67420.18181230.14762656X-RAY DIFFRACTION98
2.6742-3.06110.16661350.15872650X-RAY DIFFRACTION98
3.0611-3.85630.15171440.15372633X-RAY DIFFRACTION98
3.8563-45.58820.16841510.16922684X-RAY DIFFRACTION98
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)
10.0272-0.0616-0.02970.1703-0.01980.2104-0.1767-0.03690.179-0.27640.04130.1817-0.0234-0.1405-0.01770.12350.0101-0.01550.1399-0.00930.1429-16.23348.348-24.2645
20.16170.1396-0.00290.4332-0.04840.1167-0.111-0.01980.0163-0.37360.03110.02330.01630.0454-0.03520.1509-0.0229-0.00460.1660.00580.1483-11.049713.1886-26.7366
30.27990.15140.15360.24330.01810.31290.0524-0.0290.10860.0576-0.02860.090.06880.02440.10120.07920.00730.00930.10450.0060.124-15.2937-1.3323-15.1935
40.02770.0288-0.10650.0374-0.07890.6282-0.02540.0169-0.63810.31890.0627-0.50140.59050.49760.03140.34950.1065-0.05140.3013-0.02340.5354-3.0269-4.4307-8.7409
50.4883-0.0609-0.33250.8910.06020.29440.10420.1635-0.09990.10180.0565-0.10840.29280.28090.09560.21870.0755-0.04120.1361-0.02520.1371-11.563-10.2342-19.9996
60.33010.07740.07410.22820.05760.27540.06920.018-0.0260.1507-0.04520.00660.36830.0310.04850.2412-0.0106-0.00430.11780.00650.1277-15.9161-9.8348-14.5813
70.1791-0.1772-0.05630.49150.0760.02730.0199-0.0925-0.06390.0497-0.18020.30230.1383-0.266-0.05130.1594-0.03390.04860.1941-0.01530.1823-23.5595-4.2509-11.8649
80.12110.21410.12470.38720.12130.2281-0.01650.00860.0603-0.22620.01810.0498-0.15990.0309-0.00240.1481-0.00050.01870.1483-0.01510.1361-13.50643.9493-25.3666
90.0363-0.1033-0.0870.21670.1910.19430.0242-0.0781-0.19440.08140.04440.14060.1501-0.1523-0.01990.12230.0031-0.00370.16170.00010.1391-20.239114.2566-6.1608
100.4802-0.2832-0.43021.0368-0.10381.69570.0974-0.00880.0731-0.0198-0.0413-0.1084-0.27520.04840.07650.1194-0.009-0.00190.0991-0.0050.1164-14.978325.9899-12.9123
110.1159-0.1726-0.15390.30880.07490.2562-0.00970.0024-0.01620.32470.0406-0.03280.13690.0394-0.01320.16820.0053-0.01640.1466-0.01460.1173-15.797618.6595-2.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 56 THROUGH 68 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 69 THROUGH 84 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 85 THROUGH 106 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 107 THROUGH 119 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 120 THROUGH 131 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 132 THROUGH 168 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 169 THROUGH 184 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 185 THROUGH 208 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 54 THROUGH 68 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 69 THROUGH 184 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 185 THROUGH 207 )

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