[English] 日本語
Yorodumi
- PDB-7x8q: Frizzled-10 CRD in complex with F10_A9 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x8q
TitleFrizzled-10 CRD in complex with F10_A9 Fab
Components
  • Antibody F10_A9 Fab, Heavy chain
  • Antibody F10_A9 Fab, Light chain
  • Frizzled-10
KeywordsSIGNALING PROTEIN / Antibody
Function / homology
Function and homology information


: / Wnt receptor activity / Wnt-protein binding / Class B/2 (Secretin family receptors) / negative regulation of GTPase activity / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of JUN kinase activity / G protein-coupled receptor activity / regulation of actin cytoskeleton organization ...: / Wnt receptor activity / Wnt-protein binding / Class B/2 (Secretin family receptors) / negative regulation of GTPase activity / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of JUN kinase activity / G protein-coupled receptor activity / regulation of actin cytoskeleton organization / neuron differentiation / positive regulation of GTPase activity / cell surface / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
Frizzled-10 / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Frizzled-10 / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGe, Q. / Wang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770895 China
CitationJournal: Structure / Year: 2023
Title: An epitope-directed selection strategy facilitating the identification of Frizzled receptor selective antibodies.
Authors: Ge, Q. / Teng, M. / Li, X. / Guo, Q. / Tao, Y.
History
DepositionMar 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Frizzled-10
B: Antibody F10_A9 Fab, Light chain
C: Antibody F10_A9 Fab, Heavy chain
D: Frizzled-10
E: Antibody F10_A9 Fab, Light chain
F: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)125,5946
Polymers125,5946
Non-polymers00
Water3,189177
1
A: Frizzled-10
B: Antibody F10_A9 Fab, Light chain
C: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,7973
Polymers62,7973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-34 kcal/mol
Surface area25370 Å2
MethodPISA
2
D: Frizzled-10
E: Antibody F10_A9 Fab, Light chain
F: Antibody F10_A9 Fab, Heavy chain


Theoretical massNumber of molelcules
Total (without water)62,7973
Polymers62,7973
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-31 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.452, 156.452, 94.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

-
Components

#1: Protein Frizzled-10 / / Fz-10 / hFz10 / FzE7


Mass: 14903.371 Da / Num. of mol.: 2 / Mutation: N48Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD10 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9ULW2
#2: Antibody Antibody F10_A9 Fab, Light chain


Mass: 23231.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Antibody F10_A9 Fab, Heavy chain


Mass: 24661.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.0, 30% Jeffamine ED-2001, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→36.88 Å / Num. obs: 34538 / % possible obs: 100 % / Redundancy: 16.6 % / Biso Wilson estimate: 41.22 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.026 / Rrim(I) all: 0.108 / Χ2: 0.961 / Net I/σ(I): 29.2
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 3.75 / Num. unique obs: 1698 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.217 / Rrim(I) all: 0.905 / Χ2: 0.926 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CM4

5cm4


Resolution: 2.65→36.88 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1653 4.83 %
Rwork0.2051 32573 -
obs0.2071 34226 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.48 Å2 / Biso mean: 50.221 Å2 / Biso min: 19.23 Å2
Refinement stepCycle: final / Resolution: 2.65→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8270 0 0 177 8447
Biso mean---37.83 -
Num. residues----1080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.730.29271240.252618274298
2.73-2.820.25151150.24942700281599
2.82-2.920.31121350.25762660279599
2.92-3.030.34191490.26292665281499
3.03-3.170.33891440.250726732817100
3.17-3.340.27861490.225226922841100
3.34-3.550.26691370.224827092846100
3.55-3.820.24631450.208627042849100
3.82-4.210.23461330.187827292862100
4.21-4.810.17921430.158927612904100
4.81-6.060.21761490.178827802929100
6.06-36.880.2191300.1842882301298

+
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