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Basic information

Entry
Database: PDB / ID: 7jks
TitleCrystal structure of vaccine-elicited broadly neutralizing VRC01-class antibody 2411a in complex with HIV-1 gp120 core
Components
  • HIV-1 gp120 core
  • The heavy chain of antibody 2411a
  • The light chain of antibody 2411a
KeywordsIMMUNE SYSTEM / broadly neutralizing antibody / VRC01-class / vaccine-elicited / HIV-1
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: 3.45 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 1.2Oct 30, 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
H: The heavy chain of antibody 2411a
L: The light chain of antibody 2411a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,00311
Polymers90,8683
Non-polymers2,1358
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.920, 188.330, 45.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody The heavy chain of antibody 2411a


Mass: 25487.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody The light chain of antibody 2411a


Mass: 23543.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 13 molecules G

#1: Protein HIV-1 gp120 core


Mass: 41837.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 8 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Details

Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12 % PEG3350, 100 mM MgCl2, 2 M NaCl and 100 mM Imidazole, pH 6.5. 15 % 2R,3R-butanediol as cryoprotectant

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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: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.419→50 Å / Num. obs: 12487 / % possible obs: 91.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.065 / Rrim(I) all: 0.14 / Χ2: 1.293 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.513.30.7325030.7980.3970.8390.5275.9
3.51-3.573.40.6855100.8390.3690.7830.47576.2
3.57-3.643.30.6225400.8480.340.7120.53681.1
3.64-3.723.40.5815650.8590.3260.670.56886
3.72-3.83.60.4485600.920.2360.5090.57585.8
3.8-3.893.80.4365990.9550.2140.4880.61988.9
3.89-3.983.90.336280.9820.1630.370.61494.9
3.98-4.0940.2756290.9760.1340.3080.75995.6
4.09-4.2140.2236240.9870.1090.250.87592
4.21-4.354.10.1976360.9920.0960.220.99196.2
4.35-4.540.1896640.9890.0920.2111.21599.4
4.5-4.6840.146660.9960.0680.1571.26796.9
4.68-4.894.10.1696480.9910.0840.1891.58599.2
4.89-5.153.90.1586860.9920.080.1781.45499
5.15-5.473.70.1226710.9930.0660.141.66899.4
5.47-5.940.1136740.9930.0570.1281.52996.8
5.9-6.494.30.0926780.9970.0460.1031.64699.7
6.49-7.434.20.086840.9950.040.091.88297.6
7.43-9.353.70.0576570.9950.0320.0662.52190.9
9.35-5030.0566650.9950.0360.0673.93885.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14-3260-000refinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVS

4xvs


Resolution: 3.45→42.298 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3317 584 5.14 %
Rwork0.2828 10783 -
obs0.2852 11367 84.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.6 Å2 / Biso mean: 95.7409 Å2 / Biso min: 20.7 Å2
Refinement stepCycle: final / Resolution: 3.45→42.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 137 12 6160
Biso mean--73.65 41.15 -
Num. residues----769
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.45-3.76320.39481090.3269164053
3.7632-4.30730.32841540.2896284991
4.3073-5.4250.33561710.2741312499
5.425-42.2980.31051500.275317094
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)
10.35530.0750.07280.02080.0148-0.0041-0.0903-0.27760.8750.25140.1439-0.0506-0.24050.00060.18980.15890.60690.089-0.3228-0.61961.38677.029685.63726.6855
25.276-0.3635-1.32291.5055-0.87431.48010.4071-0.91331.14470.51220.3873-0.0903-0.3965-0.12680.3850.36010.12260.05240.38540.19761.796512.84788.731325.7876
30.0268-0.04070.04660.0587-0.07330.08810.1119-0.1379-0.1990.0462-0.0536-0.3196-0.0350.0824-0.04591.0902-0.2585-0.47810.5799-0.23161.534122.8736107.91428.7679
40.0209-0.1601-0.14341.16031.03130.9144-0.12650.67740.2395-0.0015-0.74820.05550.55780.8095-0.26491.70770.0195-0.34681.21450.75631.623346.3982107.348515.9171
50.06410.14970.07850.34410.18170.0957-0.1460.52020.2705-1.17520.3184-0.128-0.3469-0.40460.02871.2658-0.056-0.39070.90840.26931.049929.0568110.293718.5585
60.0130.0089-0.01460.0045-0.00840.01330.17660.37520.0345-0.2487-0.223-0.08340.00830.0887-01.61680.06020.01211.16740.73992.019734.5515108.11338.7069
70.60680.4248-0.2050.2968-0.14270.0689-0.0137-0.1683-0.2331-0.1143-0.0938-0.09850.23990.1024-0.07741.87280.262-0.03750.63230.19290.547827.6864102.373930.7245
80.11990.00020.3044-0.00230.00060.7752-0.35350.8923-0.0478-0.62090.1273-0.4314-0.41340.93340.04452.2862-0.32780.28871.23010.05191.033943.4705106.34148.9428
90.04810.098-0.00040.21140.08230.169-0.0496-0.3434-0.09070.83140.48150.0449-0.1726-0.8656-0.06912.5358-0.2778-0.76371.62450.67741.594936.6284117.136814.1518
100.98130.99260.38141.14430.08031.42490.41950.1279-0.97150.2718-0.2287-0.19540.305-0.04230.00190.64220.1707-0.04850.43990.00280.5794-0.467542.55719.4883
113.1626-0.05790.05210.95780.08490.61580.39611.16490.0504-0.455-0.45460.37210.46360.1098-0.09870.71790.10730.06010.5103-0.0863-0.2789-4.282153.30710.1009
120.33220.09760.02043.01350.36950.0567-0.28110.3548-0.0267-1.51420.2881-0.3552-0.0010.4857-0.06311.07110.38990.41351.47770.0393-0.18657.668457.9443-1.2276
131.39050.43150.45641.8907-0.40462.94730.47011.13810.056-0.88520.1490.10140.15240.42033.33650.87480.4459-0.0460.89440.2196-0.38957.512953.387.3954
142.5197-1.3788-1.09251.8957-0.24522.16240.36240.66111.1051-0.1896-0.0224-0.7496-0.42240.51744.2962-0.23120.94040.2185-0.0330.45490.315123.531470.674818.6691
150.63220.66560.55940.79540.57020.4943-0.33130.58870.4274-0.6495-0.36670.24780.32990.4978-0.08170.42990.23570.14790.95260.02780.591524.77567.086113.0631
161.68641.11920.70440.75560.40050.8426-0.54660.50510.5823-0.4089-0.01180.0524-0.17640.4021-0.43170.52090.08150.45010.41560.42361.238927.392979.597118.8389
173.08671.5105-2.28950.7529-1.29183.34030.3512-0.31251.1890.40930.18681.084-0.88790.5316-0.24910.5752-0.21770.17031.1880.04832.861644.7601111.931725.1768
180.0761-0.38550.45892.0534-2.40594.2703-0.05040.71930.33280.30360.3247-0.2347-0.7915-0.33940.19270.33-0.37370.02770.94230.32261.55540.779195.402424.1749
190.17310.8536-0.55884.4432-2.26742.7694-0.1244-0.37481.01781.3123-0.1341-0.0816-1.20630.28090.34330.9137-0.0752-0.37431.6631-0.4072.15442.8634108.175531.1499
200.37180.47620.20830.62380.3140.69920.1778-0.19950.3748-0.09310.08920.1922-0.73350.40440.23511.1149-0.36230.40030.78460.35452.741351.7951102.170128.0567
210.1021-0.2103-0.01920.635-0.36910.8459-0.003-0.58590.60020.44710.52940.126-0.39770.1174-0.38390.54740.12240.31390.9415-0.26571.94129.96895.51223.4458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 19 through 75 )L19 - 75
2X-RAY DIFFRACTION2chain 'L' and (resid 76 through 102 )L76 - 102
3X-RAY DIFFRACTION3chain 'L' and (resid 103 through 115 )L103 - 115
4X-RAY DIFFRACTION4chain 'L' and (resid 116 through 136 )L116 - 136
5X-RAY DIFFRACTION5chain 'L' and (resid 137 through 150 )L137 - 150
6X-RAY DIFFRACTION6chain 'L' and (resid 151 through 163 )L151 - 163
7X-RAY DIFFRACTION7chain 'L' and (resid 164 through 174 )L164 - 174
8X-RAY DIFFRACTION8chain 'L' and (resid 175 through 186 )L175 - 186
9X-RAY DIFFRACTION9chain 'L' and (resid 187 through 210 )L187 - 210
10X-RAY DIFFRACTION10chain 'G' and (resid 45 through 215 )G45 - 215
11X-RAY DIFFRACTION11chain 'G' and (resid 216 through 327 )G216 - 327
12X-RAY DIFFRACTION12chain 'G' and (resid 328 through 395 )G328 - 395
13X-RAY DIFFRACTION13chain 'G' and (resid 396 through 493 )G396 - 493
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 59 )H1 - 59
15X-RAY DIFFRACTION15chain 'H' and (resid 60 through 82 )H60 - 82
16X-RAY DIFFRACTION16chain 'H' and (resid 82A through 124 )H82
17X-RAY DIFFRACTION17chain 'H' and (resid 125 through 143 )H125 - 143
18X-RAY DIFFRACTION18chain 'H' and (resid 144 through 176 )H144 - 176
19X-RAY DIFFRACTION19chain 'H' and (resid 177 through 187 )H177 - 187
20X-RAY DIFFRACTION20chain 'H' and (resid 188 through 216 )H188 - 216
21X-RAY DIFFRACTION21chain 'L' and (resid 1 through 18 )L1 - 18

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