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- PDB-7jkt: Crystal structure of vaccine-elicited broadly neutralizing VRC01-... -

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Basic information

Entry
Database: PDB / ID: 7jkt
TitleCrystal structure of vaccine-elicited broadly neutralizing VRC01-class antibody 2413a in complex with HIV-1 gp120 core
Components
  • HIV-1 gp120 core from strain d45-01dG5
  • Heavy chain of antibody 2413a
  • Light chain of antibody 2413a
KeywordsViral Protein/Immune System / broadly neutralizing antibody / VRC01-class / vaccine-elicited / IMMUNE SYSTEM / Viral Protein-Immune System complex
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsZhou, T. / Chen, X. / Kwong, P.D. / Mascola, J.R.
CitationJournal: Immunity / Year: 2021
Title: Vaccination induces maturation in a mouse model of diverse unmutated VRC01-class precursors to HIV-neutralizing antibodies with >50% breadth.
Authors: Chen, X. / Zhou, T. / Schmidt, S.D. / Duan, H. / Cheng, C. / Chuang, G.Y. / Gu, Y. / Louder, M.K. / Lin, B.C. / Shen, C.H. / Sheng, Z. / Zheng, M.X. / Doria-Rose, N.A. / Joyce, M.G. / ...Authors: Chen, X. / Zhou, T. / Schmidt, S.D. / Duan, H. / Cheng, C. / Chuang, G.Y. / Gu, Y. / Louder, M.K. / Lin, B.C. / Shen, C.H. / Sheng, Z. / Zheng, M.X. / Doria-Rose, N.A. / Joyce, M.G. / Shapiro, L. / Tian, M. / Alt, F.W. / Kwong, P.D. / Mascola, J.R.
History
DepositionJul 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: HIV-1 gp120 core from strain d45-01dG5
H: Heavy chain of antibody 2413a
L: Light chain of antibody 2413a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,36315
Polymers90,9423
Non-polymers2,42112
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-2 kcal/mol
Surface area35920 Å2
Unit cell
Length a, b, c (Å)67.252, 67.857, 240.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy chain of antibody 2413a


Mass: 25578.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Cell (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody 2413a


Mass: 23525.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pVRC8400 / Cell (production host): 293F / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 10 molecules G

#1: Protein HIV-1 gp120 core from strain d45-01dG5


Mass: 41837.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: d45-01dG5 / Plasmid: pVRC8400 / Cell line (production host): GNTI-/- / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 34 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 5.3 % PEG 8000, 130 mM (NH4)2SO4, 100 mM HEPES, pH 7.5, and 2.2 % isopropanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 28816 / % possible obs: 97.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.048 / Rrim(I) all: 0.12 / Χ2: 1.21 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.40.61814220.8640.2840.6820.52597.7
2.8-2.855.90.5513970.8830.2440.6030.53296.1
2.85-2.960.50714580.9110.2210.5540.55799.7
2.9-2.966.10.4813710.9130.2070.5240.59195.5
2.96-3.036.20.40914370.9420.1780.4470.66999.7
3.03-3.16.10.36514320.950.1580.3990.6996.4
3.1-3.176.20.314410.9590.1310.3290.8399.4
3.17-3.265.80.27313930.9550.1230.3010.83996.8
3.26-3.365.60.21814520.9740.0980.240.99797.7
3.36-3.466.30.214130.9770.0860.2181.09698
3.46-3.596.60.16714600.9870.0690.1811.25998
3.59-3.736.60.14414540.9880.0610.1571.37199.5
3.73-3.96.40.12714410.990.0540.1391.41798.2
3.9-4.116.10.11214470.9920.050.1231.68498
4.11-4.365.80.09514530.9890.0440.1051.94697.7
4.36-4.75.20.08214500.9930.040.0922.12697.1
4.7-5.175.30.07514010.9930.0360.0831.9392.1
5.17-5.926.40.07214750.9950.0310.0791.6797.9
5.92-7.466.10.06515130.9950.0280.0711.56498.1
7.46-505.30.05415060.9960.0250.062.00491.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVS

4xvs


Resolution: 2.75→39.251 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1444 5.02 %
Rwork0.197 27325 -
obs0.1998 28769 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.64 Å2 / Biso mean: 75.9074 Å2 / Biso min: 33.09 Å2
Refinement stepCycle: final / Resolution: 2.75→39.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 151 31 6268
Biso mean--98.99 62.36 -
Num. residues----781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.84610.33141470.2739264896
2.8461-2.960.34461420.2635269398
2.96-3.09470.37051390.2626272898
3.0947-3.25780.2971450.2415269098
3.2578-3.46180.29281380.2301272298
3.4618-3.72880.30441480.2097276299
3.7288-4.10370.22661420.1878274898
4.1037-4.69670.20351450.1542274797
4.6967-5.91410.18791460.1693272495
5.9141-39.2510.25881520.1907286395
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)
16.1316-0.83382.66276.1738-2.48273.76740.0663-0.5791-0.12880.5306-0.03050.46510.15-0.8704-0.23630.6452-0.13180.090.4849-0.14330.495724.2665-18.8438-56.0238
23.48681.3528-1.18383.88580.03523.1855-0.3031-0.164-0.186-0.0181-0.00820.33910.5746-0.34910.34220.57980.0355-0.01370.4338-0.03790.45722.8764-12.5564-48.9566
32.2928-0.0953-0.00952.0990.5045.5280.02320.0250.2588-0.0379-0.1280.4524-0.1474-0.8070.06230.4430.0609-0.00760.4512-0.10870.601216.55567.299-47.8212
47.2595-1.874-0.81054.41960.81943.365-0.17220.2671-0.0325-0.23140.02990.6762-0.3433-0.29870.1810.5535-0.059-0.09950.29510.0540.512322.82519.7569-56.3918
56.61792.3063.49044.6298-0.40035.7845-0.1403-0.4880.30770.4339-0.31480.8571-0.3742-0.8280.41420.34150.05280.00480.4168-0.04980.514720.66789.5882-44.1043
69.27970.9053-1.45827.6169-4.91515.80550.1708-0.76760.221.02980.03830.82540.74430.0477-0.45010.7693-0.01090.07810.5649-0.08540.264521.3659-13.2028-41.9877
71.73340.11190.58143.83490.02153.6902-0.0655-0.03340.11580.0585-0.2058-0.1016-0.19490.2290.25280.5414-0.03690.00520.48570.0240.373841.396814.3564-34.9198
87.15671.06734.85875.4308-3.2357.4557-0.07220.0808-1.2111-0.06930.4355-0.7709-0.11640.6983-0.24030.67930.0815-0.01870.4325-0.05230.781562.765838.0856-12.6566
97.05762.98992.52631.55390.26856.0850.13720.2222-0.5452-0.1613-0.06-0.82080.12560.284-0.06720.69050.0467-0.09880.366-0.02790.941864.543538.8859-12.1249
108.92260.32235.21523.0045-0.62686.8819-0.1224-0.64630.47470.7703-0.27260.3705-0.3034-0.8310.42340.8647-0.04750.11380.4191-0.13380.499633.454710.6703-12.3946
110.83051.70940.57934.78212.02550.00470.1089-0.0457-0.06850.442-0.1879-0.3850.0401-0.00520.10560.7223-0.0722-0.02840.5740.04020.432844.182116.1587-11.3158
124.97180.53070.71923.1621-2.94495.49980.3994-0.1528-0.05220.0558-0.00090.6476-0.2203-0.2263-0.39930.5071-0.0408-0.04580.49260.05320.552350.121242.3604-3.2151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 45 through 73 )G45 - 73
2X-RAY DIFFRACTION2chain 'G' and (resid 74 through 258 )G74 - 258
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 378 )G259 - 378
4X-RAY DIFFRACTION4chain 'G' and (resid 379 through 442 )G379 - 442
5X-RAY DIFFRACTION5chain 'G' and (resid 443 through 476 )G443 - 476
6X-RAY DIFFRACTION6chain 'G' and (resid 477 through 493 )G477 - 493
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 111 )H1 - 111
8X-RAY DIFFRACTION8chain 'H' and (resid 112 through 162 )H112 - 162
9X-RAY DIFFRACTION9chain 'H' and (resid 163 through 216 )H163 - 216
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 39 )L1 - 39
11X-RAY DIFFRACTION11chain 'L' and (resid 40 through 131 )L40 - 131
12X-RAY DIFFRACTION12chain 'L' and (resid 132 through 216 )L132 - 216

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