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- PDB-7lvb: CHOLERA TOXIN B SUBUNIT WITH ATTACHED SIV EPITOPE -

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Basic information

Entry
Database: PDB / ID: 7lvb
TitleCHOLERA TOXIN B SUBUNIT WITH ATTACHED SIV EPITOPE
ComponentsCholera enterotoxin B-subunit,Surface protein gp120
KeywordsTOXIN / CHOLERA TOXIN / LECTIN / COMPLEX / GALACTOSE / SIMIAN IMMUNODEFICIENCY VIRUS / IMMUNE EPITOPE
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular region / metal ion binding
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / Enterotoxin / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
beta-D-galactopyranose / TRIETHYLENE GLYCOL / Envelope glycoprotein gp160 / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPatskovsky, Y. / Cardozo, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)272201300004I-P00005-27200007-1 United States
CitationJournal: Front Immunol / Year: 2023
Title: Cholera toxin B scaffolded, focused SIV V2 epitope elicits antibodies that influence the risk of SIV mac251 acquisition in macaques.
Authors: Rahman, M.A. / Becerra-Flores, M. / Patskovsky, Y. / Silva de Castro, I. / Bissa, M. / Basu, S. / Shen, X. / Williams, L.D. / Sarkis, S. / N'guessan, K.F. / LaBranche, C. / Tomaras, G.D. / ...Authors: Rahman, M.A. / Becerra-Flores, M. / Patskovsky, Y. / Silva de Castro, I. / Bissa, M. / Basu, S. / Shen, X. / Williams, L.D. / Sarkis, S. / N'guessan, K.F. / LaBranche, C. / Tomaras, G.D. / Aye, P.P. / Veazey, R. / Paquin-Proulx, D. / Rao, M. / Franchini, G. / Cardozo, T.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cholera enterotoxin B-subunit,Surface protein gp120
E: Cholera enterotoxin B-subunit,Surface protein gp120
F: Cholera enterotoxin B-subunit,Surface protein gp120
G: Cholera enterotoxin B-subunit,Surface protein gp120
H: Cholera enterotoxin B-subunit,Surface protein gp120
A: Cholera enterotoxin B-subunit,Surface protein gp120
B: Cholera enterotoxin B-subunit,Surface protein gp120
C: Cholera enterotoxin B-subunit,Surface protein gp120
I: Cholera enterotoxin B-subunit,Surface protein gp120
J: Cholera enterotoxin B-subunit,Surface protein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,99646
Polymers134,55210
Non-polymers4,44436
Water11,494638
1
D: Cholera enterotoxin B-subunit,Surface protein gp120
E: Cholera enterotoxin B-subunit,Surface protein gp120
F: Cholera enterotoxin B-subunit,Surface protein gp120
G: Cholera enterotoxin B-subunit,Surface protein gp120
H: Cholera enterotoxin B-subunit,Surface protein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,25521
Polymers67,2765
Non-polymers1,97916
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cholera enterotoxin B-subunit,Surface protein gp120
B: Cholera enterotoxin B-subunit,Surface protein gp120
C: Cholera enterotoxin B-subunit,Surface protein gp120
I: Cholera enterotoxin B-subunit,Surface protein gp120
J: Cholera enterotoxin B-subunit,Surface protein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74125
Polymers67,2765
Non-polymers2,46520
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.290, 112.428, 137.102
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
11D
21E
31F
41G
51H
61A
71B
81C
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 102 / Label seq-ID: 1 - 102

Dom-IDAuth asym-IDLabel asym-ID
1DA
2EB
3FC
4GD
5HE
6AF
7BG
8CH
9II
10JJ

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.989366, 0.140649, 0.037048), (-0.010315, 0.321928, -0.946708), (-0.14508, 0.936259, 0.319955)-9.07402, 80.032631, -18.18276
3given(0.97764, 0.193111, -0.083233), (0.107076, -0.797812, -0.593322), (-0.180981, 0.571143, -0.80065)-6.42011, 123.324867, 52.99538
4given(0.97771, 0.089332, -0.190009), (0.183259, -0.804742, 0.56463), (-0.102469, -0.586865, -0.803175)4.05838, 70.135094, 115.15538
5given(0.989762, -0.035748, -0.13818), (0.142412, 0.311813, 0.93941), (0.009504, -0.949471, 0.313711)8.50131, -6.98974, 82.581886
6given(0.991744, 0.018233, 0.126929), (-0.013696, 0.999239, -0.036523), (-0.127499, 0.034483, 0.991239)3.0867, -15.05762, 66.147682
7given(0.976472, 0.155525, 0.149382), (0.101712, 0.278665, -0.954987), (-0.190152, 0.947712, 0.25629)-5.68222, 13.30676, -12.14089
8given(0.977617, 0.209577, 0.018523), (0.185345, -0.816213, -0.547214), (-0.099565, 0.538399, -0.836787)-12.29319, 96.469017, -8.6375
9given(0.990393, 0.112984, -0.07972), (0.137952, -0.767773, 0.625694), (0.009487, -0.630681, -0.775984)-7.89251, 119.288597, 71.708778
10given(0.999957, -0.007216, -0.005831), (0.007997, 0.351757, 0.936057), (-0.004703, -0.936063, 0.3518)1.82864, 50.44883, 117.575142

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Components

#1: Protein
Cholera enterotoxin B-subunit,Surface protein gp120 / Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera ...Cholera enterotoxin subunit B / Cholera toxin B protein (CTB) / Cholera toxin B subunit / Cholera toxin beta subunit / Cholera toxin subunit B / Cholerae toxin B subunit / CtxB


Mass: 13455.224 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria), (gene. exp.) Simian immunodeficiency virus
Gene: ctxB, C9J66_18955, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, env
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57193, UniProt: P19503
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.07 % / Description: plates
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18-24% PEG3350, 0.1M TRIS-HCL, PH 8.0, 10MM GALACTOSE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018 / Details: Si(111) MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→29.26 Å / Num. obs: 62497 / % possible obs: 99.7 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.3
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 7191 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CT1

1ct1


Resolution: 2.25→29.26 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.499 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1863 3 %RANDOM
Rwork0.1565 ---
obs0.1577 60584 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 113.68 Å2 / Biso mean: 38.108 Å2 / Biso min: 21.64 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å20 Å20 Å2
2---19.74 Å2-0 Å2
3---13.57 Å2
Refinement stepCycle: final / Resolution: 2.25→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8497 0 238 638 9373
Biso mean--48.42 40.67 -
Num. residues----1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198889
X-RAY DIFFRACTIONr_bond_other_d0.0010.028687
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.95811955
X-RAY DIFFRACTIONr_angle_other_deg0.692320059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02725.556387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.752151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3941530
X-RAY DIFFRACTIONr_chiral_restr0.0630.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021899
Refine LS restraints NCS

Ens-ID: 1 / Number: 1566 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1DMEDIUM POSITIONAL0.280.5
2EMEDIUM POSITIONAL0.240.5
3FMEDIUM POSITIONAL0.310.5
4GMEDIUM POSITIONAL0.30.5
5HMEDIUM POSITIONAL0.280.5
6AMEDIUM POSITIONAL0.310.5
7BMEDIUM POSITIONAL0.230.5
8CMEDIUM POSITIONAL0.330.5
9IMEDIUM POSITIONAL0.260.5
0MEDIUM POSITIONAL0.290.5
1DMEDIUM THERMAL2.632
2EMEDIUM THERMAL2.192
3FMEDIUM THERMAL2.462
4GMEDIUM THERMAL2.952
5HMEDIUM THERMAL3.92
6AMEDIUM THERMAL3.052
7BMEDIUM THERMAL2.272
8CMEDIUM THERMAL2.32
9IMEDIUM THERMAL3.182
0MEDIUM THERMAL2.922
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 125 -
Rwork0.211 4413 -
all-4538 -
obs--99.82 %

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