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- PDB-1jrf: NMR Solution Structure of the Viral Receptor Domain of Tva -

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Basic information

Entry
Database: PDB / ID: 1jrf
TitleNMR Solution Structure of the Viral Receptor Domain of Tva
ComponentsSUBGROUP A ROUS SARCOMA VIRUS RECEPTORS PG800 AND PG950
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / DISULFIDE BOND / ALPHA HELIX / CALCIUM CAGE
Function / homology
Function and homology information


Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / Low-density lipoprotein receptor domain class A / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Subgroup A Rous sarcoma virus receptor pg950
Similarity search - Component
Biological speciesCoturnix japonica (Japanese quail)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Q.-Y. / Huang, W. / Dolmer, K. / Gettins, P.G.W. / Rong, L.
CitationJournal: J.Virol. / Year: 2002
Title: Solution structure of the viral receptor domain of Tva and its implications in viral entry.
Authors: Wang, Q.Y. / Huang, W. / Dolmer, K. / Gettins, P.G. / Rong, L.
History
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBGROUP A ROUS SARCOMA VIRUS RECEPTORS PG800 AND PG950
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1142
Polymers5,0741
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide SUBGROUP A ROUS SARCOMA VIRUS RECEPTORS PG800 AND PG950 / Tva LDL-A module / LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN


Mass: 5074.394 Da / Num. of mol.: 1 / Fragment: LDL-A domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix japonica (Japanese quail) / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P98162
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA, HN(CA)CB
12515N-TOCSY
1321H-15N HSQC
1432D NOESY
154(H)CCH-NOESY
165NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Tva LDL-A module U-15N 13C; 20mM CH3COOH, 10mM CaCl2, and 10% D2O, pH 5.390% H2O/10% D2O
22mM Tva LDL-A module U-15N; 20mM CD3COOD, 10mM CaCl2, and 99% D2O, pH 5.399% D2O
32mM Tva LDL-A module 14N; 20mM CH3COOH, 10mM CaCl2, and 99% D2O, pH 5.399% D2O
42mM Tva LDL-A module U-15N, 13C; 20mM CD3COOD, 10mM CaCl2, and 99% D2O, pH 5.399% D2O
52mM Tva LDL-A module U-15N; 20mM CH3COOH, 10mM CaCl2, and 10% D2O, pH 5.390% H2O/10% D2O
Sample conditionspH: 5.3 / Pressure: ambient / Temperature: 282 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DIANA1.4Guntert, P.structure solution
DIANA1.4Guntert, P.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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