[English] 日本語
Yorodumi
- PDB-6ulm: Crystal structure of human cadherin 17 EC1-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ulm
TitleCrystal structure of human cadherin 17 EC1-2
ComponentsCadherin-17
KeywordsCELL ADHESION / cdh17 / intestinal epithelia / cancer / calcium-binding
Function / homology
Function and homology information


oligopeptide transmembrane transport / positive regulation of integrin activation by cell surface receptor linked signal transduction / proton-dependent oligopeptide secondary active transmembrane transporter activity / marginal zone B cell differentiation / germinal center B cell differentiation / oligopeptide transport / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions ...oligopeptide transmembrane transport / positive regulation of integrin activation by cell surface receptor linked signal transduction / proton-dependent oligopeptide secondary active transmembrane transporter activity / marginal zone B cell differentiation / germinal center B cell differentiation / oligopeptide transport / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / spleen development / integrin-mediated signaling pathway / adherens junction / cell morphogenesis / beta-catenin binding / integrin binding / cell migration / cell junction / basolateral plasma membrane / cell adhesion / cadherin binding / calcium ion binding / cell surface / nucleoplasm / plasma membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGray, M.E. / Sotomayor, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism.
Authors: Gray, M.E. / Sotomayor, M.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Cadherin-17
A: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6228
Polymers51,3812
Non-polymers2406
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, assay for oligomerization, bead aggregation assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8114
Polymers25,6911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8114
Polymers25,6911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.394, 81.609, 106.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B10 - 212
2111A10 - 212

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.968254, 0.186706, 0.166207), (-0.197243, -0.97912, -0.049178), (0.153555, -0.0804, 0.984864)1.53952, -2.01017, 14.21636

-
Components

#1: Protein Cadherin-17 / Intestinal peptide-associated transporter HPT-1 / Liver-intestine cadherin / LI-cadherin


Mass: 25690.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH17 / Variant: VAR_055567 / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q12864
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7, 0.1 M KCl, 15% PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 28521 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.46
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1406 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q2V

3q2v


Resolution: 2.15→47.53 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.68 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1412 5 %RANDOM
Rwork0.2062 ---
obs0.2087 26913 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 30.462 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20 Å2
2---0.38 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 2.15→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 6 203 3388
Biso mean--24.38 30.89 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133256
X-RAY DIFFRACTIONr_bond_other_d00.0172936
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6544430
X-RAY DIFFRACTIONr_angle_other_deg1.1971.5676863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3215403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26124.246179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631516
X-RAY DIFFRACTIONr_chiral_restr0.0560.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.023657
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02627
Refine LS restraints NCSNumber: 1534 / Type: TIGHT THERMAL / Rms dev position: 4.84 Å / Weight position: 0.5
LS refinement shellResolution: 2.15→2.205 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 105 -
Rwork0.265 1939 -
all-2044 -
obs--98.84 %
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)
10.89150.68271.1150.58160.67342.06320.1434-0.25950.00240.0978-0.2245-0.01030.1727-0.30070.08110.0512-0.0154-0.01630.1056-0.01410.018812.866-7.19323.556
20.3709-0.04560.34940.2888-0.02340.8642-0.0108-0.0204-0.0185-0.04320.01090.0109-0.0157-0.0055-0.00010.0162-0.0012-0.02470.0027-0.00030.07523.621-9.385-21.952
30.58250.5990.06371.0290.97136.06690.1288-0.08910.1303-0.01650.0020.0928-0.12370.1138-0.13080.081-0.04970.03930.0347-0.02570.0358-9.3296.2158.959
40.2097-0.0639-0.12160.692-0.51541.28150.03280.0376-0.0364-0.0189-0.00390.04480.0407-0.0271-0.02880.0184-0.0017-0.01030.01370.00250.0497-6.04510.736-35.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 97
2X-RAY DIFFRACTION1B301 - 302
3X-RAY DIFFRACTION2B98 - 212
4X-RAY DIFFRACTION2B303
5X-RAY DIFFRACTION3A10 - 97
6X-RAY DIFFRACTION3A301 - 302
7X-RAY DIFFRACTION4A98 - 214
8X-RAY DIFFRACTION4A303

+
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