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- PDB-7knv: Solution NMR structure of CDHR3 extracellular domain EC1 -

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Basic information

Entry
Database: PDB / ID: 7knv
TitleSolution NMR structure of CDHR3 extracellular domain EC1
ComponentsCadherin-related family member 3
KeywordsCELL ADHESION / receptor
Function / homology
Function and homology information


cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / synaptic cleft / axon terminus / synaptic transmission, glutamatergic / adherens junction ...cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / synaptic cleft / axon terminus / synaptic transmission, glutamatergic / adherens junction / cell morphogenesis / virus receptor activity / cadherin binding / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Cadherin-related family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, W. / Tonelli, M. / Frederick, R.O. / Watters, K.E. / Markley, J.L. / Palmenberg, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103399 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19-AI070503 United States
CitationJournal: Viruses / Year: 2021
Title: Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1
Authors: Lee, W. / Frederick, R.O. / Tonelli, M. / Palmenberg, A.C.
History
DepositionNov 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-related family member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8094
Polymers13,6881
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area220 Å2
ΔGint-24 kcal/mol
Surface area8590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cadherin-related family member 3 / Cadherin-like protein 28


Mass: 13688.275 Da / Num. of mol.: 1 / Fragment: Extracellular domain EC1, residues 21-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDHR3, CDH28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZTQ4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1141isotropic12D 1H-15N HSQC
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic23D HN(CA)CO
161isotropic23D HNCO
171isotropic23D HBHA(CO)NH
181isotropic23D (H)CCH-TOCSY
191isotropic33D (H)CCH-TOCSY
1101isotropic33D (H)CCH-COSY
1111isotropic23D NOESY 1H-15N HSQC
1121isotropic23D NOESY 1H-13C HSQC aliphatic
1131isotropic32D 1H-13C HSQC aliphatic

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-100% 13C; U-100% 15N] CDHR3 extracellular domain EC1, 50 mM HEPES, 300 mM potassium chloride, 10 mM calcium chloride, 0.05 % w/v sodium azide, 10 % v/v [U-100% 2H] D2O, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMCDHR3 extracellular domain EC1[U-100% 13C; U-100% 15N]1
50 mMHEPESnatural abundance1
300 mMpotassium chloridenatural abundance1
10 mMcalcium chloridenatural abundance1
0.05 % w/vsodium azidenatural abundance1
10 % v/vD2O[U-100% 2H]1
Sample conditionsIonic strength: 380 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Varian VNMRVarianVNMR6002
Varian VNMRVarianVNMR8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYLee, Tonelli, Markleypeak picking
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
PONDEROSA-C/SLee, Petit, Cornilescu, Stark and Markleystructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing5
simulated annealing6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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