[English] 日本語
Yorodumi
- PDB-5fwv: Wnt modulator Kremen crystal form III at 3.2A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fwv
TitleWnt modulator Kremen crystal form III at 3.2A
ComponentsKREMEN PROTEIN 1
KeywordsSIGNALING PROTEIN / WNT / CELL SURFACE / SIGNALLING / MEMBRANE PROTEIN
Function / homology
Function and homology information


Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / limb development / regulation of canonical Wnt signaling pathway / negative regulation of ossification / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / limb development / regulation of canonical Wnt signaling pathway / negative regulation of ossification / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / transmembrane signaling receptor activity / neuronal cell body / apoptotic process / signal transduction / membrane / plasma membrane
Similarity search - Function
Kremen / : / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. ...Kremen / : / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å
AuthorsZebisch, M. / Jackson, V.A. / Jones, E.Y.
CitationJournal: Structure / Year: 2016
Title: Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf
Authors: Zebisch, M. / Jackson, V.A. / Zhao, Y. / Jones, E.Y.
History
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Other / Structure summary
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KREMEN PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1718
Polymers44,5521
Non-polymers6207
Water362
1
A: KREMEN PROTEIN 1
hetero molecules

A: KREMEN PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,34316
Polymers89,1042
Non-polymers1,23914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3100 Å2
ΔGint-54.2 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.844, 67.844, 198.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1324-

CL

-
Components

#1: Protein KREMEN PROTEIN 1


Mass: 44551.777 Da / Num. of mol.: 1 / Fragment: ECD, RESIDUES 29-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q96MU8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.6 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES/MOPS 7.5 30 % P550MME_P20K DRIED OUT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→67.8 Å / Num. obs: 8171 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 22.7 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 13.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.2→64.19 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.864 / SU B: 53.731 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26484 376 4.6 %RANDOM
Rwork0.19549 ---
obs0.1988 7732 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 3.2→64.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 33 2 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192419
X-RAY DIFFRACTIONr_bond_other_d0.0030.022091
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9363296
X-RAY DIFFRACTIONr_angle_other_deg1.09634822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31123.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4161513
X-RAY DIFFRACTIONr_chiral_restr0.10.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
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_it2.2374.361175
X-RAY DIFFRACTIONr_mcbond_other2.2294.361174
X-RAY DIFFRACTIONr_mcangle_it3.8836.5351467
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3714.6681244
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: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 25 -
Rwork0.323 487 -
obs--90.78 %
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)
12.1671-1.95131.59283.0077-1.19211.9046-0.1522-0.126-0.14590.37580.23650.5290.0775-0.5314-0.08420.25480.0732-0.00420.18820.05550.18272.362521.801832.1761
26.1168-2.52660.01752.9939-0.08185.3841-0.18910.0923-0.2157-0.01020.03730.1030.2807-0.59350.15180.0801-0.0845-0.00750.15850.00350.02071.413515.88937.1239
33.04274.2725-1.261910.6686-0.13115.5280.2923-0.48850.23490.7486-0.0046-0.2582-0.24730.2437-0.28770.4268-0.0983-0.06810.2976-0.03140.178414.368438.83789.074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 117
2X-RAY DIFFRACTION2A118 - 212
3X-RAY DIFFRACTION3A213 - 322

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more