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- PDB-5dd0: Crystal structures in an anti-HIV antibody lineage from immunizat... -

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Basic information

Entry
Database: PDB / ID: 5dd0
TitleCrystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques
Components
  • ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN
  • ANTI-HIV ANTIBODY DH570 FAB HEAVY LIGHT
  • oligo peptide
KeywordsIMMUNE SYSTEM / HIV HIV-1 gp41 MPER antibody
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsZhang, R. / Verkoczy, L. / Wiehe, K. / Alam, S.M. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C. / Gao, F. / Montefiori, D.C. ...Zhang, R. / Verkoczy, L. / Wiehe, K. / Alam, S.M. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / Parks, R. / Foulger, A. / Tomaras, G. / Keple, T.B. / Moody, M.A. / Liao, H.-X. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI100645-02 United States
CitationJournal: Sci Transl Med / Year: 2016
Title: Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages.
Authors: Zhang, R. / Verkoczy, L. / Wiehe, K. / Munir Alam, S. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C.W. / Zhang, J. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / ...Authors: Zhang, R. / Verkoczy, L. / Wiehe, K. / Munir Alam, S. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C.W. / Zhang, J. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / Larimore, K. / Greenberg, P.D. / Parks, R. / Foulger, A. / Peel, J.N. / Luo, K. / Lu, X. / Trama, A.M. / Vandergrift, N. / Tomaras, G.D. / Kepler, T.B. / Moody, M.A. / Liao, H.X. / Haynes, B.F.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 1.5Oct 30, 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: ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN
L: ANTI-HIV ANTIBODY DH570 FAB HEAVY LIGHT
P: oligo peptide


Theoretical massNumber of molelcules
Total (without water)49,2583
Polymers49,2583
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.332, 80.406, 37.861
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN


Mass: 24783.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293, Expi293 / Production host: Homo sapiens (human)
#2: Antibody ANTI-HIV ANTIBODY DH570 FAB HEAVY LIGHT


Mass: 23075.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293, Expi293 / Production host: Homo sapiens (human)
#3: Protein/peptide oligo peptide


Mass: 1398.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK293, Expi293 / Production host: Homo sapiens (human) / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 1500, 20% glycerol, with seeding

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15105 / % possible obs: 100 % / Redundancy: 4.6 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6G, 2QQN

3q6g

2qqn


Resolution: 2.488→24.373 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 1515 10.03 %
Rwork0.2273 --
obs0.2322 15105 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.488→24.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 68 3437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033477
X-RAY DIFFRACTIONf_angle_d0.7184746
X-RAY DIFFRACTIONf_dihedral_angle_d13.4181217
X-RAY DIFFRACTIONf_chiral_restr0.027549
X-RAY DIFFRACTIONf_plane_restr0.003596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4884-2.56860.35921350.32331138X-RAY DIFFRACTION93
2.5686-2.66030.37281320.30531257X-RAY DIFFRACTION100
2.6603-2.76670.34451370.28061230X-RAY DIFFRACTION100
2.7667-2.89240.32771390.27231259X-RAY DIFFRACTION100
2.8924-3.04470.33281400.25741198X-RAY DIFFRACTION100
3.0447-3.2350.31061370.25551256X-RAY DIFFRACTION100
3.235-3.48410.29271410.231240X-RAY DIFFRACTION100
3.4841-3.83360.32721340.24691257X-RAY DIFFRACTION100
3.8336-4.38550.20181430.19711221X-RAY DIFFRACTION100
4.3855-5.51470.17341420.15671255X-RAY DIFFRACTION100
5.5147-24.37410.22381350.16751279X-RAY DIFFRACTION100
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)
10.90060.36440.42710.4318-0.19081.279-0.21880.56310.0796-0.19190.5204-0.11980.04230.64810.21840.3174-0.07680.00420.42740.04640.22137.989221.456984.3302
20.61960.13160.94391.78510.45463.08910.29890.14880.6251-0.234-0.38180.90370.07290.10270.08930.2847-0.0281-0.0760.1659-0.00020.375529.797321.460791.0558
31.5334-0.0630.60361.6267-0.23351.1829-0.0075-0.0489-0.03150.00220.12630.07210.01150.2417-0.13370.17920.01070.04180.2256-0.00840.200236.370120.907595.5213
41.0853-0.21440.9030.6779-0.70721.873-0.01080.3641-0.0387-0.099-0.00980.0310.1653-0.05090.00880.26480.02030.05560.2661-0.02440.258510.770119.600565.9641
50.64380.16211.06970.7977-0.59963.2684-0.02440.0459-0.29580.0523-0.11280.0958-0.24990.29710.07610.17190.03290.07010.17980.05170.402213.484533.024696.8927
61.3984-0.3990.73471.40410.0641.5231-0.04030.07530.1937-0.0287-0.056-0.0549-0.2107-0.14320.05910.21940.0199-0.010.1911-0.02340.193624.284835.587298.0032
71.01510.2690.17770.7490.47720.9219-0.1395-0.02090.01770.02740.15250.1344-0.3103-0.04040.00690.2217-0.0068-0.04220.2335-0.00040.189520.947634.230597.9346
80.2944-0.21920.07870.5338-0.41370.3983-0.2259-0.1303-0.05460.1264-0.167-0.4853-0.02560.0574-1.38370.29370.165-0.2343-0.0164-0.01520.47753.576536.337483.8904
91.04980.08470.15183.51091.04681.4727-0.14930.1091-0.28330.08760.1878-0.03960.07750.1801-0.11540.23760.05560.00950.2906-0.01110.2676-1.776318.124873.356
101.63880.7887-0.14890.44040.01810.14260.0684-0.6511-0.4668-0.1833-0.3129-0.3607-0.00520.06280.11040.31740.0167-0.02180.30080.04870.3013-2.712712.132880.5893
111.08060.10360.26471.85720.3811.2574-0.0976-0.0223-0.00380.17730.160.15950.008-0.0907-0.0620.2470.0054-0.01180.2950.03530.2582-4.09319.510275.5014
123.8894-0.4877-0.78333.11770.05072.0186-0.0707-0.04330.7093-0.21570.25160.4296-0.33210.7221-0.04510.20290.0111-0.02350.3144-0.07240.290246.096825.961106.4469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'H' and (resid 33 through 44 )
3X-RAY DIFFRACTION3chain 'H' and (resid 45 through 118 )
4X-RAY DIFFRACTION4chain 'H' and (resid 119 through 228 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 18 )
6X-RAY DIFFRACTION6chain 'L' and (resid 19 through 61 )
7X-RAY DIFFRACTION7chain 'L' and (resid 62 through 102 )
8X-RAY DIFFRACTION8chain 'L' and (resid 103 through 113 )
9X-RAY DIFFRACTION9chain 'L' and (resid 114 through 150 )
10X-RAY DIFFRACTION10chain 'L' and (resid 151 through 163 )
11X-RAY DIFFRACTION11chain 'L' and (resid 164 through 211 )
12X-RAY DIFFRACTION12chain 'P' and (resid 660 through 670 )

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