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- PDB-5u3o: Crystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MP... -

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Basic information

Entry
Database: PDB / ID: 5u3o
TitleCrystal Structure of DH511.2_K3 Fab in Complex with HIV-1 gp41 MPER Peptide
Components
  • DH511.2_K3 Fab Heavy Chain
  • DH511.2_K3 Fab Light Chain
  • gp41 MPER peptide
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / Neutralizing / Antibody / gp41 / MPER / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated suppression of host complement activation by recruitment of complement control protein / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsOfek, G. / Wu, L. / Lougheed, C.S. / Williams, L.D. / Nicely, N.I. / Haynes, B.F.
CitationJournal: Sci Immunol / Year: 2017
Title: Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.
Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I. ...Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I.S. / Seaman, M.S. / Parks, R.J. / Marshall, D.J. / Anasti, K. / Yang, G. / Nie, X. / Tumba, N.L. / Wiehe, K. / Wagh, K. / Korber, B. / Kepler, T.B. / Munir Alam, S. / Morris, L. / Kamanga, G. / Cohen, M.S. / Bonsignori, M. / Xia, S.M. / Montefiori, D.C. / Kelsoe, G. / Gao, F. / Mascola, J.R. / Moody, M.A. / Saunders, K.O. / Liao, H.X. / Tomaras, G.D. / Georgiou, G. / Haynes, B.F.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 4, 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DH511.2_K3 Fab Heavy Chain
L: DH511.2_K3 Fab Light Chain
A: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)52,1543
Polymers52,1543
Non-polymers00
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-29 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.721, 101.857, 176.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-515-

HOH

21L-438-

HOH

31L-502-

HOH

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Components

#1: Antibody DH511.2_K3 Fab Heavy Chain


Mass: 25420.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Heavy Chain / Production host: Homo sapiens (human) / Variant (production host): HEK 293
#2: Antibody DH511.2_K3 Fab Light Chain


Mass: 23943.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Light Chain / Production host: Homo sapiens (human) / Variant (production host): HEK 293
#3: Protein/peptide gp41 MPER peptide


Mass: 2789.345 Da / Num. of mol.: 1 / Fragment: gp41 656-683 / Source method: obtained synthetically / Details: gp41 MPER Peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q73372*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 7% Isopropanol, 20% PEG 3350, 0.2 M Ammonium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→30.876 Å / Num. obs: 55786 / % possible obs: 98.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.89 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.056 / Rrim(I) all: 0.128 / Χ2: 1.045 / Net I/σ(I): 9.7 / Num. measured all: 285952
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
1.76-1.83.60.59651520.713179.9
1.8-1.854.80.5740.812199.9
1.85-1.95.30.5290.862199.9
1.9-1.955.20.4920.8971100
1.95-2.015.30.3640.926199.9
2.01-2.095.20.3210.944199.9
2.09-2.175.20.2580.96199.8
2.17-2.275.20.2360.963199.9
2.27-2.395.30.1980.973199.9
2.39-2.545.40.1620.9791100
2.54-2.735.30.1390.983199.9
2.73-3.015.20.1110.988199.8
3.01-3.445.10.0910.992199.8
3.44-4.345.10.0730.993199.8
4.34-505.30.0610.994198.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3L

5u3l


Resolution: 1.761→30.876 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 1995 3.58 %
Rwork0.1611 --
obs0.1622 55779 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.761→30.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 0 512 4132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053738
X-RAY DIFFRACTIONf_angle_d0.7585092
X-RAY DIFFRACTIONf_dihedral_angle_d15.262215
X-RAY DIFFRACTIONf_chiral_restr0.051560
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7608-1.80480.30721300.22843429X-RAY DIFFRACTION91
1.8048-1.85360.26091500.20133841X-RAY DIFFRACTION100
1.8536-1.90810.24171200.17773832X-RAY DIFFRACTION100
1.9081-1.96970.19861550.16983840X-RAY DIFFRACTION100
1.9697-2.04010.20821400.16253812X-RAY DIFFRACTION100
2.0401-2.12170.18561470.16773840X-RAY DIFFRACTION100
2.1217-2.21830.20161460.16153862X-RAY DIFFRACTION100
2.2183-2.33520.20011360.16123820X-RAY DIFFRACTION100
2.3352-2.48150.18291440.15853889X-RAY DIFFRACTION100
2.4815-2.67290.2021430.16243864X-RAY DIFFRACTION100
2.6729-2.94170.20261380.16493873X-RAY DIFFRACTION100
2.9417-3.3670.18421470.15633899X-RAY DIFFRACTION100
3.367-4.24030.17391400.14433946X-RAY DIFFRACTION100
4.2403-30.88110.17291590.1584037X-RAY DIFFRACTION99
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)
17.0966-2.17122.09162.6431-0.53960.91-0.0935-0.17860.1536-0.3576-0.2210.0969-0.1689-0.22360.12820.45330.2627-0.0870.4452-0.08140.2249-27.44611.2858-38.573
23.0255-0.17370.47772.8076-0.07353.8798-0.02590.3330.064-0.2410.1376-0.3156-0.41610.3028-0.09220.20240.00130.0250.1435-0.0150.26581.25080.058-19.7206
32.32720.12051.14391.16150.23021.51830.0420.25350.1338-0.3355-0.0535-0.0738-0.3287-0.0833-0.00330.29190.10010.0230.20690.00490.1474-10.0909-0.1524-26.7543
42.48871.6018-0.27282.08491.94858.92480.0025-0.0520.0636-0.0609-0.14570.1144-0.0131-0.4005-0.1970.19910.10650.01290.2128-0.03540.2459-12.06311.7192-17.8769
52.96-0.86130.29542.46410.85950.43290.02550.13560.1448-0.24610.21660.0374-0.1359-0.1710.10130.2040.06530.03450.1367-0.01580.1766-5.41862.7019-18.3866
63.86670.39862.24930.23460.17761.31390.04360.37960.0467-0.1793-0.0304-0.0342-0.132-0.04810.06540.19480.1236-0.04120.2744-0.02560.0932-19.1707-6.6384-33.316
74.36190.25082.96980.91730.65383.83480.02310.3699-0.0847-0.19140.0576-0.0641-0.21440.0426-0.05540.23550.06180.02220.1731-0.00420.1754-7.2896-6.6943-27.7219
81.2004-0.54910.14232.27430.49270.9092-0.09340.00960.0552-0.08380.0277-0.0413-0.04550.04760.02330.11550.0286-0.02360.1101-0.01260.163916.3551-24.4095-8.9864
93.1426-2.6742-0.90835.75031.28691.5011-0.05080.15120.3009-0.0148-0.026-0.8049-0.00250.1598-0.05090.09550.0023-0.02510.1398-0.01470.221625.3818-22.8073-10.2386
104.65241.911-0.44342.3855-0.26170.33770.1234-0.2342-0.24840.4644-0.2315-0.2891-0.00810.06850.18440.1990.0235-0.07060.2024-0.04730.221424.9107-25.3316-3.7157
116.7676-5.3635-2.01154.85561.3171.5419-0.1953-0.0597-0.20880.23930.16460.14150.3089-0.23350.03390.1952-0.0273-0.03430.2262-0.0220.2027-14.5275-24.9782-28.0604
124.6172-2.83433.03813.3079-0.1524.29310.03960.26820.2683-0.00040.0609-0.5949-0.27170.238-0.04470.12390.0384-0.00360.1643-0.04040.1714-5.7044-15.8654-32.3596
131.3697-1.0657-0.22832.31031.30172.69040.13360.00490.1203-0.0053-0.0727-0.0538-0.0193-0.3826-0.06530.15750.0059-0.01460.18660.00090.1646-12.0405-19.7091-32.788
143.2487-2.45671.9992.0861-2.36214.41030.07380.1962-0.0474-0.1245-0.0798-0.14030.12680.0118-0.0410.17420.0295-0.04120.1168-0.05190.16382.8127-35.7673-25.3207
151.21360.82241.26072.69292.9267.0545-0.0297-0.0667-0.07630.0484-0.02450.02710.0970.2143-0.04930.09610.0448-0.01290.1269-0.00730.190813.2532-31.0441-2.3969
160.63990.20220.19590.78341.34082.32860.0028-0.0401-0.0721-0.1034-0.07610.11220.0017-0.36450.14260.14240.0333-0.00710.1737-0.02850.2120.6325-35.2336-9.7241
170.9530.3333-0.3831.72331.03166.0151-0.01750.0493-0.0744-0.25440.0362-0.0105-0.18570.2842-0.05180.08590.0392-0.01520.1343-0.02510.21274.799-30.7791-11.1252
181.29910.31181.52091.45821.37292.5801-0.0208-0.18710.02620.0507-0.06990.086-0.2732-0.31750.1550.09870.03320.00380.1277-0.01830.16257.7568-29.10051.5652
192.30260.92411.85521.9981.6593.04760.0099-0.2236-0.13580.1827-0.0084-0.0090.6698-0.0724-0.16740.2191-0.00670.0150.15490.01330.20346.3296-40.6109-1.4706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 669 through 685 )
2X-RAY DIFFRACTION2chain 'H' and (resid 1 through 17 )
3X-RAY DIFFRACTION3chain 'H' and (resid 18 through 59 )
4X-RAY DIFFRACTION4chain 'H' and (resid 60 through 72 )
5X-RAY DIFFRACTION5chain 'H' and (resid 73 through 87 )
6X-RAY DIFFRACTION6chain 'H' and (resid 88 through 100)
7X-RAY DIFFRACTION7chain 'H' and (resid 101 through 111 )
8X-RAY DIFFRACTION8chain 'H' and (resid 112 through 188 )
9X-RAY DIFFRACTION9chain 'H' and (resid 189 through 203 )
10X-RAY DIFFRACTION10chain 'H' and (resid 204 through 216 )
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 32 )
12X-RAY DIFFRACTION12chain 'L' and (resid 33 through 48 )
13X-RAY DIFFRACTION13chain 'L' and (resid 49 through 102 )
14X-RAY DIFFRACTION14chain 'L' and (resid 103 through 113 )
15X-RAY DIFFRACTION15chain 'L' and (resid 114 through 139 )
16X-RAY DIFFRACTION16chain 'L' and (resid 140 through 150 )
17X-RAY DIFFRACTION17chain 'L' and (resid 151 through 172 )
18X-RAY DIFFRACTION18chain 'L' and (resid 173 through 188 )
19X-RAY DIFFRACTION19chain 'L' and (resid 189 through 214 )

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