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- PDB-5u3j: Crystal Structure of DH511.1 Fab in Complex with HIV-1 gp41 MPER ... -

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Basic information

Entry
Database: PDB / ID: 5u3j
TitleCrystal Structure of DH511.1 Fab in Complex with HIV-1 gp41 MPER Peptide
Components
  • DH511.1 Heavy Chain
  • DH511.1 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


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / plasma 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 / molecular replacement / Resolution: 2.74 Å
AuthorsOfek, G. / Wu, L. / Lougheed, C.S. / Williams, L.D. / Nicely, N.I. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5UM1AII00645 United States
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 1.1Aug 23, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / software
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: DH511.1 Heavy Chain
L: DH511.1 Light Chain
A: gp41 MPER peptide


Theoretical massNumber of molelcules
Total (without water)53,4803
Polymers53,4803
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-29 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.092, 133.963, 179.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-314-

HOH

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Components

#1: Antibody DH511.1 Heavy Chain


Mass: 25314.432 Da / Num. of mol.: 1 / Fragment: Fragment of antigen binding
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Heavy Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody DH511.1 Light Chain


Mass: 23537.135 Da / Num. of mol.: 1 / Fragment: Fragment of antigen binding
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG Light Chain / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Protein/peptide gp41 MPER peptide


Mass: 4628.267 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: V9QIE5*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1500

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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: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→37.295 Å / Num. obs: 20466 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 66.59 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.8 / Num. unique all: 1711 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3P

5u3p


Resolution: 2.74→37.3 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.264 998 4.88 %
Rwork0.229 --
obs0.231 20457 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 95.21 Å2
Refinement stepCycle: LAST / Resolution: 2.74→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 0 23 3688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023774
X-RAY DIFFRACTIONf_angle_d0.4995139
X-RAY DIFFRACTIONf_dihedral_angle_d10.2452228
X-RAY DIFFRACTIONf_chiral_restr0.041570
X-RAY DIFFRACTIONf_plane_restr0.003652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.738-2.88230.39051220.33622454X-RAY DIFFRACTION88
2.8823-3.06280.31691700.29462774X-RAY DIFFRACTION100
3.0628-3.29910.30681290.26762784X-RAY DIFFRACTION100
3.2991-3.63090.30141550.24382799X-RAY DIFFRACTION100
3.6309-4.15570.28341430.22182829X-RAY DIFFRACTION100
4.1557-5.23340.21791400.18792843X-RAY DIFFRACTION100
5.2334-37.29840.23321390.21992976X-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)
14.50120.21311.3272.76470.13454.52060.1218-0.2082-0.0282-0.0761-0.07150.1221-0.07810.3004-0.07910.3335-0.0176-0.03880.51890.02580.3413-40.803258.575622.3182
21.7942-0.4954-0.05791.5469-0.5521.9596-0.0484-0.2905-0.1253-0.1950.19410.50190.0599-0.4422-0.19890.469-0.0553-0.17280.59250.06590.5655-48.78851.264713.8653
34.0197-1.97820.31326.7792-0.00251.59040.21370.0442-0.1018-0.3679-0.6173-0.53040.22420.2450.36610.5760.0285-0.01030.9570.20980.6328-17.203935.185136.5174
41.6338-0.3237-0.68022.50321.84281.40470.0875-0.05790.1426-0.76110.0452-1.20430.29360.6076-0.10610.62130.105-0.0431.02780.32160.9662-9.323832.6636.9955
52.3185-1.21530.63123.5517-1.08242.65110.38920.1963-0.4616-0.75060.20090.50591.0075-0.5252-0.33130.9778-0.0629-0.43950.5630.02390.5698-46.309436.915512.7
61.6491-1.22450.87222.6487-1.16912.34270.57910.2291-0.51-0.7962-0.37710.24640.6280.3351-0.04220.63590.0209-0.17530.62320.05390.5356-33.96733.494625.4193
71.38840.8646-1.85833.16092.13156.57540.1637-0.1793-0.8340.28340.2290.78440.2065-0.28920.03750.52280.1107-0.36080.61430.00391.1172-27.90724.106431.4429
83.854-0.2014-0.36353.60.08024.47860.5032-0.7867-0.3571-0.54590.01430.5887-0.15580.2088-0.13320.50080.0529-0.14340.73380.20090.6951-29.128626.98835.1216
92.35571.52150.75956.25153.28188.05130.2078-0.6919-0.82440.2816-0.17220.39580.603-0.1982-0.1110.42910.0611-0.1220.73740.21040.8281-27.172221.838945.8048
102.4009-2.1037-1.54878.1809-5.10887.89530.4346-0.1460.86250.0667-0.361-0.682-1.49821.47740.46530.792-0.0639-0.03240.89110.05110.3893-48.04372.94280.3479
112.80633.95320.03696.48912.39125.95220.16030.82931.43581.08580.46560.80130.3465-0.61760.15930.5515-0.0139-0.13811.02290.13070.6444-62.225259.30936.61
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND (RESID 1 THROUGH 93 )
2X-RAY DIFFRACTION2CHAIN 'H' AND (RESID 94 THROUGH 114 )
3X-RAY DIFFRACTION3CHAIN 'H' AND (RESID 115 THROUGH 176 )
4X-RAY DIFFRACTION4CHAIN 'H' AND (RESID 177 THROUGH 215 )
5X-RAY DIFFRACTION5CHAIN 'L' AND (RESID 1 THROUGH 75 )
6X-RAY DIFFRACTION6CHAIN 'L' AND (RESID 76 THROUGH 130 )
7X-RAY DIFFRACTION7CHAIN 'L' AND (RESID 131 THROUGH 145 )
8X-RAY DIFFRACTION8CHAIN 'L' AND (RESID 146 THROUGH 176 )
9X-RAY DIFFRACTION9CHAIN 'L' AND (RESID 177 THROUGH 213 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 659 THROUGH 671 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 672 THROUGH 684 )

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