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- PDB-8g8a: Crystal structure of DH1317.8 Fab in complex with HIV proximal MP... -

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Basic information

Entry
Database: PDB / ID: 8g8a
TitleCrystal structure of DH1317.8 Fab in complex with HIV proximal MPER peptide
Components
  • DH1317.8 heavy chain
  • DH1317.8 light chain
  • Env polyprotein
KeywordsIMMUNE SYSTEM / HIV / Neutralizing Antibody / MPER / gp41
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsJanus, B.M. / Astavans, A. / Ofek, G.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Cell / Year: 2024
Title: Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans.
Authors: Williams, W.B. / Alam, S.M. / Ofek, G. / Erdmann, N. / Montefiori, D.C. / Seaman, M.S. / Wagh, K. / Korber, B. / Edwards, R.J. / Mansouri, K. / Eaton, A. / Cain, D.W. / Martin, M. / Hwang, J. ...Authors: Williams, W.B. / Alam, S.M. / Ofek, G. / Erdmann, N. / Montefiori, D.C. / Seaman, M.S. / Wagh, K. / Korber, B. / Edwards, R.J. / Mansouri, K. / Eaton, A. / Cain, D.W. / Martin, M. / Hwang, J. / Arus-Altuz, A. / Lu, X. / Cai, F. / Jamieson, N. / Parks, R. / Barr, M. / Foulger, A. / Anasti, K. / Patel, P. / Sammour, S. / Parsons, R.J. / Huang, X. / Lindenberger, J. / Fetics, S. / Janowska, K. / Niyongabo, A. / Janus, B.M. / Astavans, A. / Fox, C.B. / Mohanty, I. / Evangelous, T. / Chen, Y. / Berry, M. / Kirshner, H. / Van Itallie, E. / Saunders, K.O. / Wiehe, K. / Cohen, K.W. / McElrath, M.J. / Corey, L. / Acharya, P. / Walsh, S.R. / Baden, L.R. / Haynes, B.F.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DH1317.8 heavy chain
B: DH1317.8 light chain
H: DH1317.8 heavy chain
L: DH1317.8 light chain
C: Env polyprotein
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,76012
Polymers100,2266
Non-polymers5346
Water77543
1
A: DH1317.8 heavy chain
B: DH1317.8 light chain
C: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3344
Polymers50,1133
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: DH1317.8 heavy chain
L: DH1317.8 light chain
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4268
Polymers50,1133
Non-polymers3135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.976, 63.840, 111.971
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 8 molecules AHBLCP

#1: Protein DH1317.8 heavy chain


Mass: 24009.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody DH1317.8 light chain


Mass: 23599.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Env polyprotein


Mass: 2503.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q69910
#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.: 2 / 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 , 2 types, 47 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20.1% Isopropanol, 10.05% PEG 8000, and 0.1M Imidazole/Hydrochloric acid pH 6.5

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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: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 40649 / % possible obs: 94.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.8
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.61 / Num. unique obs: 3324 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NRX

4nrx


Resolution: 2.44→41.89 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2000 4.93 %
Rwork0.2221 --
obs0.2238 40608 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6823 0 32 43 6898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.848
X-RAY DIFFRACTIONf_dihedral_angle_d12.5882480
X-RAY DIFFRACTIONf_chiral_restr0.0761085
X-RAY DIFFRACTIONf_plane_restr0.0051216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.44591100.43912126X-RAY DIFFRACTION74
2.5-2.570.43311300.39512511X-RAY DIFFRACTION86
2.57-2.650.38341390.3492679X-RAY DIFFRACTION93
2.65-2.730.37361450.32972794X-RAY DIFFRACTION97
2.73-2.830.34991440.30752780X-RAY DIFFRACTION96
2.83-2.940.3191460.29582811X-RAY DIFFRACTION96
2.94-3.080.31971470.30482840X-RAY DIFFRACTION99
3.08-3.240.33281470.2822849X-RAY DIFFRACTION98
3.24-3.440.28821460.24432823X-RAY DIFFRACTION97
3.44-3.710.26521460.23052825X-RAY DIFFRACTION97
3.71-4.080.26511490.2192854X-RAY DIFFRACTION98
4.08-4.670.20061480.17832856X-RAY DIFFRACTION97
4.67-5.880.19921500.1722924X-RAY DIFFRACTION100
5.88-41.890.20741530.17382936X-RAY DIFFRACTION97
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)
18.23142.6127-7.96847.0879-1.50668.4927-0.8787-1.1758-1.36291.4892-0.0394-0.38720.78081.37140.72870.7760.1655-0.15550.71580.1110.600868.094613.43529.6066
29.3763.93631.50429.1433-0.56396.61570.3306-0.68980.07350.7538-0.187-0.969-0.15341.0375-0.14610.5472-0.02270.0890.6245-0.06550.585275.315618.189621.7761
35.98431.4984-1.76575.229-0.26219.18040.5543-0.63061.23660.4995-0.24790.0227-1.69510.7194-0.27481.0166-0.12840.26130.54060.01380.661569.630324.507522.9931
49.05663.4453-1.46377.3337-0.68334.35410.6247-0.07981.18170.4405-0.14070.6729-1.26230.1197-0.47170.7552-0.03480.06970.35980.07380.599565.682719.422822.0671
59.25144.2429-4.50459.1732-4.55245.7032-0.48590.3233-0.3218-1.2187-0.1212-1.02080.69550.6230.50590.6081-0.01590.15140.4077-0.04010.533270.535218.007914.6428
61.36430.5806-0.45066.21910.36822.516-0.36560.0491-0.8113-0.2445-0.0676-0.98321.30860.38960.40381.03350.11320.35730.54420.03760.909360.9057-8.835728.0741
78.66957.24231.32188.14250.73844.5160.342-0.8866-2.34060.5318-0.7102-2.52870.8160.20450.39521.42680.25870.21810.76040.28571.128664.7479-13.497834.7047
86.946-1.3778-1.00188.97141.86787.6304-0.04781.15320.3922-1.4737-0.12560.25720.0042-1.58720.14470.7149-0.1138-0.05640.89820.17360.452958.097212.2588-0.4498
96.90970.8935-1.66476.64750.246510.5497-0.08570.5601-0.1503-1.3476-0.0219-0.61570.53060.10130.08670.69310.03180.14850.44630.00980.477768.945914.20361.7105
105.32983.1478-0.07322.24930.723510.0521-0.01350.1764-0.0886-0.6075-0.19460.16830.064-0.53520.17860.50550.04110.14270.55220.10240.489764.525514.91376.0087
113.96334.279-0.32844.3713-0.1867-0.0278-0.80942.3809-0.4457-1.2068-0.00850.822.0029-1.8490.39611.825-0.6660.34850.857-0.44750.852255.8483-5.81783.4714
123.28640.16380.69181.05161.72433.6614-0.22340.1916-0.53810.03150.39630.12230.2136-0.1635-0.17621.4168-0.20940.38270.5854-0.07851.014949.3517-14.10222.7146
134.2756-0.4377-1.85962.93310.87936.6246-0.6770.3956-0.8091-0.62010.30370.38341.182-0.78190.36261.0564-0.19650.24530.5731-0.14150.927446.0284-14.651821.0429
143.1801-0.267-1.17762.51010.705110.43290.16250.43040.1489-0.2687-0.17660.6472-0.3275-1.41090.00620.56020.0579-0.03110.5988-0.14170.65819.84617.470624.872
156.8698-0.3095-0.75453.40050.44012.41730.09050.06550.3840.2376-0.1011-0.0781-0.0175-0.08840.00740.73360.02480.16380.3847-0.01590.412131.478525.694946.466
168.40260.63261.72131.1746-0.04072.4631-0.27510.9863-1.481-0.32640.2371-0.03480.6262-0.14160.04961.0028-0.08250.18310.5492-0.17380.626626.68842.811516.4101
177.9588-0.73882.23650.6012-0.56997.4366-0.32720.38510.7055-0.0064-0.1339-0.0146-0.9770.23290.46830.8853-0.03540.06560.3635-0.00880.511228.286716.009815.0433
186.3199-1.02250.23161.6690.03431.9874-0.22741.0738-0.6638-0.72360.0810.03120.0362-0.19540.16650.8479-0.10580.08880.5419-0.13470.450125.45196.699715.7169
196.45113.71046.44813.67472.20746.03220.05560.4985-0.8496-0.22680.3881-0.647-0.13260.3939-0.34380.6583-0.00210.17380.4291-0.06870.544842.24147.891230.7723
202.09970.1908-1.20621.8114-0.22348.21160.3125-0.1160.2623-0.0688-0.0828-0.0943-0.56250.0705-0.21810.5899-0.07790.1270.36260.01310.433937.228112.933652.3665
212.2538-0.6367-2.15942.15590.6866.07090.0144-0.2150.104-0.0924-0.0707-0.1983-0.41440.42330.03190.495-0.10150.05470.35820.00750.497740.5312.971651.9375
226.8689-4.46422.42366.06984.00849.87870.4407-1.43982.5724-0.9903-0.0863-1.0130.50590.1354-0.30661.6197-0.30380.44520.7943-0.23851.146578.381532.952210.9983
237.22851.05671.76986.06590.99577.2371-1.5077-1.18430.92990.10561.77830.84860.7560.7106-0.4380.78670.2393-0.08591.62210.00810.77854.636211.64814.8325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 213 )
14X-RAY DIFFRACTION14chain 'H' and (resid 1 through 119 )
15X-RAY DIFFRACTION15chain 'H' and (resid 120 through 216 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 38 )
17X-RAY DIFFRACTION17chain 'L' and (resid 39 through 61 )
18X-RAY DIFFRACTION18chain 'L' and (resid 62 through 101 )
19X-RAY DIFFRACTION19chain 'L' and (resid 102 through 113 )
20X-RAY DIFFRACTION20chain 'L' and (resid 114 through 163 )
21X-RAY DIFFRACTION21chain 'L' and (resid 164 through 214 )
22X-RAY DIFFRACTION22chain 'C' and (resid 655 through 668 )
23X-RAY DIFFRACTION23chain 'P' and (resid 656 through 670 )

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