[English] 日本語
Yorodumi
- PDB-8e0r: Crystal structure of mouse APCDD1 in P21 space group -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8e0r
TitleCrystal structure of mouse APCDD1 in P21 space group
ComponentsProtein APCDD1
KeywordsSIGNALING PROTEIN / cell signaling protein / beta barrel / lipid binding protein
Function / homology
Function and homology information


regulation of odontogenesis of dentin-containing tooth / astrocyte cell migration / Wnt-protein binding / negative regulation of Wnt signaling pathway / hair follicle development / Wnt signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
APCDD1 domain / Protein APCDD1 / Adenomatosis polyposis coli down-regulated 1 / Adenomatosis polyposis coli down-regulated 1
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsHsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure of WNT inhibitor adenomatosis polyposis coli down-regulated 1 (APCDD1), a cell-surface lipid-binding protein.
Authors: Hsieh, F.L. / Chang, T.H. / Gabelli, S.B. / Nathans, J.
History
DepositionAug 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein APCDD1
B: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6497
Polymers107,5432
Non-polymers1,1065
Water6,738374
1
A: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4354
Polymers53,7711
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein APCDD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2143
Polymers53,7711
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.861, 144.128, 64.381
Angle α, β, γ (deg.)90.000, 99.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 50 - 468 / Label seq-ID: 27 - 445

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Protein APCDD1 / Adenomatosis polyposis coli down-regulated 1 protein homolog


Mass: 53771.316 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 27-482)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apcdd1, Drapc1 / Plasmid: pHLsec / Production host: Homo sapiens (human) / References: UniProt: Q3U128
#2: 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.: 5 / Source method: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.947→34.364 Å / Num. obs: 49930 / % possible obs: 91.1 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.057 / Net I/σ(I): 8.5
Reflection shellResolution: 1.947→2.12 Å / Rmerge(I) obs: 1.464 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2486 / CC1/2: 0.56 / Rpim(I) all: 0.58

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.82 Å34.36 Å
Translation4.82 Å34.36 Å

-
Processing

Software
NameVersionClassification
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8E0P

8e0p


Resolution: 1.95→34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.349 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : TLS ONLY HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 2405 4.8 %RANDOM
Rwork0.2092 ---
obs0.2111 47515 76.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.1 Å2 / Biso mean: 9.798 Å2 / Biso min: 1.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.12 Å2
2---0.01 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.95→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 70 377 7103
Biso mean--18.4 38.27 -
Num. residues----823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137035
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176305
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6639578
X-RAY DIFFRACTIONr_angle_other_deg1.1911.58614524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.545836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20621.162413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.498151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8291555
X-RAY DIFFRACTIONr_chiral_restr0.060.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021748
Refine LS restraints NCS

Ens-ID: 1 / Number: 12634 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 13 -
Rwork0.353 257 -
all-270 -
obs--5.61 %
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)
10.4046-0.05320.08260.92090.21161.4096-0.012-0.007-0.1290.0985-0.04150.03360.10120.06140.05340.0324-0.00750.0220.00950.00030.053714.91613.254116.3738
21.182-0.1785-0.14121.134-0.07960.96180.0842-0.17960.17690.0746-0.05530.0317-0.03540.0077-0.02890.0244-0.0260.00870.0385-0.02570.036139.291950.220819.8726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 480
2X-RAY DIFFRACTION2B50 - 470

+
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