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- PDB-8g8c: Crystal structure of DH1322.1 Fab in complex with HIV proximal MP... -

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Basic information

Entry
Database: PDB / ID: 8g8c
TitleCrystal structure of DH1322.1 Fab in complex with HIV proximal MPER peptide
Components
  • DH1322.1 heavy chain
  • DH1322.1 light chain
  • Env polyprotein
KeywordsIMMUNE SYSTEM / HIV / Neutralizing Antibody / MPER / gp41
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / 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: 2.08 Å
AuthorsNiyongabo, A. / Janus, B.M. / 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
H: DH1322.1 heavy chain
L: DH1322.1 light chain
A: DH1322.1 heavy chain
B: DH1322.1 light chain
C: Env polyprotein
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3059
Polymers102,2766
Non-polymers1,0293
Water5,332296
1
H: DH1322.1 heavy chain
L: DH1322.1 light chain
C: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9465
Polymers51,1383
Non-polymers8082
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-15 kcal/mol
Surface area20770 Å2
MethodPISA
2
A: DH1322.1 heavy chain
B: DH1322.1 light chain
P: Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3594
Polymers51,1383
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-26 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.308, 182.950, 84.414
Angle α, β, γ (deg.)90.00, 92.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody / Protein/peptide / Non-polymers , 4 types, 302 molecules HALBCP

#1: Protein DH1322.1 heavy chain


Mass: 24715.607 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 DH1322.1 light chain


Mass: 23546.180 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: 2876.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A4UIY1
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 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.: 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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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 1500 and 0.1M SPG buffer pH 8.5

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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: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→28.7 Å / Num. obs: 65739 / % possible obs: 96.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13
Reflection shellResolution: 2.08→2.16 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 5860

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→28.68 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 2023 3.08 %
Rwork0.1993 --
obs0.2002 65718 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6933 0 67 296 7296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.166
X-RAY DIFFRACTIONf_dihedral_angle_d13.2712536
X-RAY DIFFRACTIONf_chiral_restr0.0641101
X-RAY DIFFRACTIONf_plane_restr0.011250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.33281300.30033860X-RAY DIFFRACTION82
2.14-2.190.30611320.28134593X-RAY DIFFRACTION98
2.19-2.260.29181510.27294675X-RAY DIFFRACTION99
2.26-2.330.30981510.25794594X-RAY DIFFRACTION99
2.33-2.410.28691470.23614651X-RAY DIFFRACTION99
2.41-2.510.26121410.22314592X-RAY DIFFRACTION98
2.51-2.630.25131440.22534513X-RAY DIFFRACTION97
2.63-2.760.28991470.23624656X-RAY DIFFRACTION99
2.76-2.940.25251500.22594645X-RAY DIFFRACTION99
2.94-3.160.28441460.22884626X-RAY DIFFRACTION99
3.16-3.480.26121450.21214607X-RAY DIFFRACTION98
3.48-3.980.20441410.18174472X-RAY DIFFRACTION95
3.98-5.010.16621490.14344633X-RAY DIFFRACTION98
5.02-28.680.19531490.18384578X-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)
15.59690.31780.02247.3801-2.85924.2485-0.08640.2182-0.8104-0.3920.0757-1.02870.4010.17720.1680.3257-0.02790.07110.4657-0.15130.7219-17.0157-66.91619.2095
23.88752.0179-1.23666.8893-1.66534.0149-0.39640.5005-1.2625-0.91470.0562-0.74110.71570.0470.27640.4103-0.02920.13930.3929-0.11690.711-24.6489-73.426210.5818
31.75491.38730.87781.63550.15060.7081-0.06140.10770.02390.0214-0.00680.1872-0.211-0.17070.08150.41340.0350.0610.44120.06250.2789-19.1813-39.943114.2162
42.01072.09211.08253.4313.1014.3457-0.020.0782-0.03690.11670.12960.0129-0.0626-0.1747-0.09580.41270.06210.03180.490.06010.2805-14.4774-43.15215.2567
52.75612.71941.87719.04586.2637.49070.1262-0.26530.23580.8735-0.00370.1658-0.0311-0.2884-0.0750.50230.02670.10020.45180.00810.3203-16.2877-34.059424.0197
62.8537-1.4454-2.28287.00467.48249.57980.20390.1350.2439-0.6127-0.12-0.085-0.91960.251-0.09080.4144-0.00060.04160.36540.07750.2398-8.9603-32.50214.6287
72.1091-7.3198-1.2188.1142.17516.41840.4776-0.86811.890.97550.0065-0.4866-0.71350.2859-0.6190.8212-0.12550.08390.4152-0.11890.795113.6405-9.097129.9111
85.0017-2.29390.96541.0994-0.08684.1982-0.12280.1925-0.44170.772-0.06070.00051.1635-0.13720.08160.8509-0.0930.14760.41380.12471.0825-31.2685-88.916726.899
93.27432.58360.21018.037-1.44645.72530.2228-0.3021-0.39170.8212-0.1569-1.05850.3430.7896-0.08480.46030.1095-0.1720.5245-0.1170.436422.7811-30.463435.4159
102.0090.16120.42294.9030.94751.50490.255-0.3415-0.06810.7866-0.0041-0.04360.0929-0.1579-0.30160.4399-0.0274-0.03570.4225-0.03340.259113.9503-30.170332.2515
114.13191.30210.01284.7764-1.01094.20.458-0.1846-1.09591.1114-0.3765-1.4830.48510.6913-0.1730.6314-0.0449-0.33750.5240.0790.986614.0097-62.5326.1566
124.0693-1.9462-3.06467.40167.4388.17270.08170.29990.3457-0.5681-0.16740.1548-0.6842-0.13350.12140.38280.065-0.07380.52430.04240.28533.8954-31.66410.799
133.41281.4632-0.27317.67243.56026.0897-0.00810.32890.0923-0.34690.265-0.2442-0.2870.5144-0.33030.2442-0.0341-0.01560.40820.00550.249414.532-26.065614.8697
142.46120.9749-0.47687.16483.78655.69570.03320.31890.2577-0.38770.06130.2162-0.3604-0.0784-0.0410.21750.0104-0.01450.34190.04180.20539.7832-27.230513.9097
152.28071.85110.02734.03212.24351.31160.09410.336-0.5832-0.1748-0.2059-0.30790.0237-0.11310.02840.28530.0324-0.01460.4391-0.09120.38423.7829-53.915913.4829
162.81111.40870.63455.1677-1.71116.42740.5754-0.7908-0.68441.3733-0.6787-0.11420.6570.4711-0.03280.8741-0.2224-0.1310.57810.05650.6812.3293-66.443128.9763
172.28312.2405-0.43316.3863-1.74244.31170.1490.0524-0.25670.4518-0.07620.5571-0.0115-0.0577-0.10260.3369-0.00560.0080.3526-0.08940.4054-3.4168-55.868915.903
183.85474.22680.01365.9967-0.40112.26230.7326-0.28570.00741.2424-0.71951.1350.4794-0.2069-0.1290.7644-0.04380.19730.5402-0.09930.6912-7.5577-58.815325.7988
193.02692.93060.05336.9667-1.48814.69910.3778-0.0365-0.64250.7694-0.27050.0140.426-0.3565-0.07190.4586-0.0252-0.00230.4067-0.12930.5888-2.2616-62.869319.7496
203.40181.8414-1.65616.39210.11224.90220.1121-0.2725-0.66080.309-0.0779-0.02160.1147-0.21-0.08630.30990.0231-0.0050.35230.13110.5045-36.3429-71.509326.4763
214.63891.8407-0.88555.5742-1.7888.36230.08960.08620.57080.2722-0.04940.7902-0.5048-0.7955-0.03490.35820.09010.09120.4606-0.06120.4027-31.0513-35.615518.2202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'B' and (resid 19 through 98 )
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 140 through 172 )
5X-RAY DIFFRACTION5chain 'B' and (resid 173 through 188 )
6X-RAY DIFFRACTION6chain 'B' and (resid 189 through 213 )
7X-RAY DIFFRACTION7chain 'C' and (resid 655 through 670 )
8X-RAY DIFFRACTION8chain 'P' and (resid 655 through 672 )
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 33 )
10X-RAY DIFFRACTION10chain 'H' and (resid 34 through 132 )
11X-RAY DIFFRACTION11chain 'H' and (resid 133 through 211 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 25 )
13X-RAY DIFFRACTION13chain 'L' and (resid 26 through 61 )
14X-RAY DIFFRACTION14chain 'L' and (resid 62 through 98 )
15X-RAY DIFFRACTION15chain 'L' and (resid 99 through 121 )
16X-RAY DIFFRACTION16chain 'L' and (resid 122 through 137 )
17X-RAY DIFFRACTION17chain 'L' and (resid 138 through 150 )
18X-RAY DIFFRACTION18chain 'L' and (resid 151 through 163 )
19X-RAY DIFFRACTION19chain 'L' and (resid 164 through 213 )
20X-RAY DIFFRACTION20chain 'A' and (resid 1 through 111 )
21X-RAY DIFFRACTION21chain 'A' and (resid 112 through 212 )

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