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- PDB-1lcs: RECEPTOR-BINDING DOMAIN FROM SUBGROUP B FELINE LEUKEMIA VIRUS -

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Basic information

Entry
Database: PDB / ID: 1lcs
TitleRECEPTOR-BINDING DOMAIN FROM SUBGROUP B FELINE LEUKEMIA VIRUS
ComponentsFELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
KeywordsVIRAL PROTEIN / antiparallel beta-sandwich glycoprotein
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Viral Glycoprotein Gp70 / ENV polyprotein, receptor-binding domain / F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / : / Envelope glycoprotein
Similarity search - Component
Biological speciesFeline leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBarnett, A.L. / Wensel, D.L. / Li, W. / Fass, D. / Cunningham, J.M.
CitationJournal: J.Virol. / Year: 2003
Title: Structure and Mechanism of a Coreceptor for Infection by a pathogenic feline retrovirus
Authors: Barnett, A.L. / Wensel, D.L. / Li, W. / Fass, D. / Cunningham, J.M.
History
DepositionApr 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
B: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2107
Polymers46,8202
Non-polymers2,3895
Water3,207178
1
A: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4234
Polymers23,4101
Non-polymers1,0133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7863
Polymers23,4101
Non-polymers1,3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules

B: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules

A: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules

A: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,41914
Polymers93,6414
Non-polymers4,77910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation8_666x-y+1,-y+1,-z+11
Buried area12690 Å2
ΔGint32 kcal/mol
Surface area39700 Å2
MethodPISA
4
B: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules

A: FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2107
Polymers46,8202
Non-polymers2,3895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area5940 Å2
ΔGint22 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 93.400, 231.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

21A-599-

HOH

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Components

#1: Protein FELINE LEUKEMIA VIRUS RECEPTOR-BINDING DOMAIN


Mass: 23410.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline leukemia virus / Genus: Gammaretrovirus / Strain: strain B/lambda-B1 / Gene: ENV / Plasmid: PVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 AND HI5 / References: GenBank: 323911, UniProt: P11261*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-2DManpb1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5][a2122h-1a_1-5_2*NCC/3=O]/1-1-2-3-4/a4-b1_b4-c1_c6-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{[(2+1)][a-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium acetate1reservoir
20.1 Mtrisodium citrate dihydrate1reservoirpH5.6
330 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21072 / Num. obs: 21010 / % possible obs: 99.7 % / Redundancy: 9 % / Rsym value: 0.061 / Net I/σ(I): 25.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 9.4 / Rsym value: 0.192 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 21072 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 100 % / Rmerge(I) obs: 0.192

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOL

1aol


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 1494 random
Rwork0.216 --
all-21072 -
obs-21010 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 159 178 3539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.32
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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