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- PDB-7r73: Crystal structure of llama VHH antibody D7 in complex with HIV-1 ... -

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Basic information

Entry
Database: PDB / ID: 7r73
TitleCrystal structure of llama VHH antibody D7 in complex with HIV-1 gp120 core
Components
  • Glycoprotein 120
  • Llama antibody D7
KeywordsIMMUNE SYSTEM / Llama / antibody / VHH / HIV-1 / gp120
Biological speciesHuman immunodeficiency virus 1
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Structure / Year: 2022
Title: Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site.
Authors: Tongqing Zhou / Lei Chen / Jason Gorman / Shuishu Wang / Young D Kwon / Bob C Lin / Mark K Louder / Reda Rawi / Erik-Stephane D Stancofski / Yongping Yang / Baoshan Zhang / Anna Forsman ...Authors: Tongqing Zhou / Lei Chen / Jason Gorman / Shuishu Wang / Young D Kwon / Bob C Lin / Mark K Louder / Reda Rawi / Erik-Stephane D Stancofski / Yongping Yang / Baoshan Zhang / Anna Forsman Quigley / Laura E McCoy / Lucy Rutten / Theo Verrips / Robin A Weiss / / Nicole A Doria-Rose / Lawrence Shapiro / Peter D Kwong /
Abstract: Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies ...Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Glycoprotein 120
A: Llama antibody D7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73710
Polymers53,9682
Non-polymers1,7708
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint20 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.543, 61.954, 63.976
Angle α, β, γ (deg.)90.000, 108.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycoprotein 120


Mass: 40068.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody Llama antibody D7


Mass: 13899.256 Da / Num. of mol.: 1 / Fragment: VHH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: 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.: 8 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M to Tris HCl pH 8.5 and 21% PEG8000. Cryoprotectant is 20% ethylend glycol with N-protone oil

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 44467 / % possible obs: 92.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 33.85 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Χ2: 1.026 / Net I/σ(I): 16.7 / Num. measured all: 147850
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.791.80.35816970.7830.290.4640.82553.2
1.79-1.8420.32622350.8030.2540.4160.85170.4
1.84-1.892.30.29626680.880.2190.370.92183.6
1.89-1.942.60.26429490.8690.1870.3251.02492.6
1.94-230.23330690.9220.1540.281.02797
2-2.073.40.19931230.9550.1240.2351.0198.7
2.07-2.163.60.17231810.9660.1040.2011.0799.4
2.16-2.263.70.1431850.9760.0840.1631.07199.7
2.26-2.383.80.12131840.9830.0720.1411.03299.7
2.38-2.523.80.10531870.9840.0630.1221.05399.9
2.52-2.723.80.09232030.9840.0550.1081.06100
2.72-2.993.80.08531870.9860.0510.0991.08399.9
2.99-3.433.80.0832260.9890.0480.0931.00199.9
3.43-4.323.70.06532190.9910.040.0771.02399.9
4.32-503.50.0631540.9870.0380.0720.97795.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T33

5t33


Resolution: 1.76→31.44 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 2238 5.03 %
Rwork0.1794 42218 -
obs0.1812 44456 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.46 Å2 / Biso mean: 59.0958 Å2 / Biso min: 24.78 Å2
Refinement stepCycle: final / Resolution: 1.76→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 194 156 3604
Biso mean--80.36 50.5 -
Num. residues----413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.80.3593600.28141253131344
1.8-1.840.31421040.2521873197766
1.84-1.880.24921130.23572327244080
1.88-1.930.29231390.22762567270690
1.93-1.990.27371410.22572738287996
1.99-2.060.21071370.20122825296298
2.06-2.130.19911480.20352845299399
2.13-2.210.20661580.19612852301099
2.21-2.310.22211510.189228312982100
2.31-2.440.22361620.202328463008100
2.44-2.590.26261610.198128803041100
2.59-2.790.25311630.193128773040100
2.79-3.070.20871380.18928843022100
3.07-3.510.20361570.178728803037100
3.51-4.420.18781730.1528873060100
4.42-31.440.2151330.16462853298696
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)
12.2988-2.3714-2.20519.47246.0394.9466-0.07590.0621-0.0244-0.03650.00550.0481-0.0181-0.2250.08590.22440.0093-0.00080.3729-0.00680.2307-21.2205-14.163130.4663
28.0101-3.4079-0.29724.0244.02966.31020.56120.75790.0013-0.7533-0.7811-0.1398-0.3761-0.93230.28420.37740.09120.08380.3640.10920.273-27.3766-3.403834.8805
37.7309-1.10361.47985.6026-1.02076.77640.4219-0.2884-0.43420.1326-0.4065-0.5790.62310.2296-0.04670.419-0.12170.01410.42520.07550.4591-39.9941-30.099420.0722
45.45771.4040.6117.77251.21645.0503-0.15190.53670.7054-0.72150.11620.7316-0.5177-0.44890.02070.3685-0.00820.0590.37620.11230.4493-46.7495-18.14179.6299
55.2684-6.60863.83349.8456-3.79053.8294-0.0537-1.10540.16840.06120.50820.17220.3103-0.7488-0.53760.3372-0.07260.03160.40860.00280.3786-33.9232-22.884924.1859
65.85520.7348-2.33985.74520.48235.0836-0.17140.47820.1998-0.20230.2085-0.18610.14290.1866-0.08410.2756-0.1173-0.05940.31730.01050.323-39.5421-22.339912.5375
77.48231.43451.43220.8540.33151.6681-0.16030.32950.408-0.19060.24390.2129-0.0767-0.0602-0.09570.3093-0.08710.0080.36730.07810.3272-38.5233-18.994310.3348
85.8289-0.2423-0.86048.19050.2854.1881-0.18020.7660.2976-0.18920.2380.26590.1892-0.052-0.03880.2913-0.15790.02050.41050.02350.2347-24.6888-15.96167.2012
95.2896-1.9988-0.16568.0323-2.05395.2277-0.02181.33510.0491-1.08650.14560.31960.25640.0907-0.02330.4535-0.24080.03390.75310.0010.2564-17.6946-14.8566-0.0357
105.9472-1.75682.17847.5228-4.87133.364-0.26590.51780.8470.88160.0690.2714-1.33360.19830.20250.4522-0.07770.0430.38030.07270.4102-17.1404-3.73097.5854
114.81510.0645-0.59053.9977-3.24543.7108-0.20940.3597-0.4745-0.49580.0054-0.30280.27830.29150.24850.2598-0.04390.06240.3511-0.0870.2895-13.8611-22.092913.7225
124.7253-0.4464-0.70266.0238-0.26444.5788-0.18440.3360.1356-0.15410.2708-0.3007-0.1110.3401-0.03250.2576-0.10230.02890.4223-0.04060.2285-16.3125-14.01889.9074
136.6806-1.74443.04744.6017-1.33923.5637-0.44430.29420.55010.00710.23030.5376-0.01530.01830.2520.3793-0.12610.0540.25450.02230.4726-39.6331-16.108515.247
144.9412-0.8683-0.19694.92165.42559.4337-0.19940.0661-0.06480.65880.14840.26620.6001-0.20010.19410.31860.08470.04920.3921-0.02720.2587-29.7776-4.766343.997
153.4631-1.1506-0.9785.4621.90984.92550.03550.19170.3856-0.00980.0714-0.2596-0.0603-0.2667-0.10470.19510.04740.00080.35410.01610.2571-21.1731-8.7435.4358
166.23561.74650.46342.55073.81766.7061-0.0809-0.34020.25631.0621-0.07680.72611.0005-0.43450.13510.49940.05340.03490.3889-0.00410.3345-23.401-15.077943.9121
173.9386-0.5468-0.53887.22392.86344.59240.1768-0.12380.57640.7412-0.1168-0.3107-0.0917-0.0541-0.10650.26760.1022-0.04050.3916-0.03680.3484-22.2305-2.773544.487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 106 )A88 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 123 )A107 - 123
3X-RAY DIFFRACTION3chain 'G' and (resid 45 through 73 )G45 - 73
4X-RAY DIFFRACTION4chain 'G' and (resid 74 through 98 )G74 - 98
5X-RAY DIFFRACTION5chain 'G' and (resid 99 through 114 )G99 - 114
6X-RAY DIFFRACTION6chain 'G' and (resid 115 through 235 )G115 - 235
7X-RAY DIFFRACTION7chain 'G' and (resid 236 through 258 )G236 - 258
8X-RAY DIFFRACTION8chain 'G' and (resid 259 through 327 )G259 - 327
9X-RAY DIFFRACTION9chain 'G' and (resid 328 through 352 )G328 - 352
10X-RAY DIFFRACTION10chain 'G' and (resid 353 through 368 )G353 - 368
11X-RAY DIFFRACTION11chain 'G' and (resid 369 through 412 )G369 - 412
12X-RAY DIFFRACTION12chain 'G' and (resid 413 through 473 )G413 - 473
13X-RAY DIFFRACTION13chain 'G' and (resid 474 through 491 )G474 - 491
14X-RAY DIFFRACTION14chain 'A' and (resid 2 through 24 )A2 - 24
15X-RAY DIFFRACTION15chain 'A' and (resid 25 through 66 )A25 - 66
16X-RAY DIFFRACTION16chain 'A' and (resid 67 through 75 )A67 - 75
17X-RAY DIFFRACTION17chain 'A' and (resid 76 through 87 )A76 - 87

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