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- PDB-5wdf: Crystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp... -

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Basic information

Entry
Database: PDB / ID: 5wdf
TitleCrystal structure of 10E8v4-5R+100cF Fab in complex with HIV-1 gp41 peptide
Components
  • 10E8v4-5R+100cF Fab heavy chain
  • FA10E8v4-5R+100cF FAB light chain
  • HIV-1 gp41 peptide
KeywordsIMMUNE SYSTEM / HIV-1 neutralizing antibody / MPER / 10E8
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 / host cell endosome membrane / actin filament organization ...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 / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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: 3.1 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Cell Rep / Year: 2018
Title: Surface-Matrix Screening Identifies Semi-specific Interactions that Improve Potency of a Near Pan-reactive HIV-1-Neutralizing Antibody.
Authors: Kwon, Y.D. / Chuang, G.Y. / Zhang, B. / Bailer, R.T. / Doria-Rose, N.A. / Gindin, T.S. / Lin, B. / Louder, M.K. / McKee, K. / O'Dell, S. / Pegu, A. / Schmidt, S.D. / Asokan, M. / Chen, X. / ...Authors: Kwon, Y.D. / Chuang, G.Y. / Zhang, B. / Bailer, R.T. / Doria-Rose, N.A. / Gindin, T.S. / Lin, B. / Louder, M.K. / McKee, K. / O'Dell, S. / Pegu, A. / Schmidt, S.D. / Asokan, M. / Chen, X. / Choe, M. / Georgiev, I.S. / Jin, V. / Pancera, M. / Rawi, R. / Wang, K. / Chaudhuri, R. / Kueltzo, L.A. / Manceva, S.D. / Todd, J.P. / Scorpio, D.G. / Kim, M. / Reinherz, E.L. / Wagh, K. / Korber, B.M. / Connors, M. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Nov 13, 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: 10E8v4-5R+100cF Fab heavy chain
L: FA10E8v4-5R+100cF FAB light chain
A: 10E8v4-5R+100cF Fab heavy chain
B: FA10E8v4-5R+100cF FAB light chain
P: HIV-1 gp41 peptide
Q: HIV-1 gp41 peptide


Theoretical massNumber of molelcules
Total (without water)100,7586
Polymers100,7586
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.284, 60.953, 70.149
Angle α, β, γ (deg.)103.08, 107.46, 100.05
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 10E8v4-5R+100cF Fab heavy chain


Mass: 25169.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 1GHG1 / Plasmid: pVRC8400 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#2: Antibody FA10E8v4-5R+100cF FAB light chain


Mass: 22879.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLC2 / Plasmid: pVRC8400 / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 gp41 peptide


Mass: 2330.745 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG3350, 10% iso-propanol, 0.1M Ammonium citrate, pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 18005 / % possible obs: 93.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.1 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5iq9

5iq9


Resolution: 3.1→45.121 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2811 743 5.16 %
Rwork0.2468 --
obs0.2486 14394 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→45.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 0 0 6558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026738
X-RAY DIFFRACTIONf_angle_d0.6059160
X-RAY DIFFRACTIONf_dihedral_angle_d3.9013946
X-RAY DIFFRACTIONf_chiral_restr0.043988
X-RAY DIFFRACTIONf_plane_restr0.0051161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.33950.31361330.2942605X-RAY DIFFRACTION88
3.3395-3.67540.33011450.27842753X-RAY DIFFRACTION94
3.6754-4.20690.31021530.27032811X-RAY DIFFRACTION96
4.2069-5.2990.26631530.23312770X-RAY DIFFRACTION95
5.299-45.12590.25841590.22772712X-RAY DIFFRACTION93
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)
15.31311.677-0.07497.24872.34452.81780.2944-0.44020.51640.5676-0.0510.88710.04470.1632-0.21620.49590.08480.19520.6346-0.01860.65-25.75711.3504-57.5304
22.1528-0.08790.23243.90273.21266.48660.74730.61250.6783-0.8985-0.2724-0.1541-0.4124-0.3565-0.43471.51110.0190.13170.90360.03610.60332.073524.8336-46.7704
37.93881.5547-0.06676.86460.46367.31590.11450.5876-0.7379-0.20.0652-0.730.46880.7975-0.15530.52630.2638-0.00770.58450.03920.5954-9.2501-8.807-63.8539
47.497-2.6618-2.42777.81486.74745.6987-0.0648-0.028-0.23380.48540.4693-0.3729-0.35440.8742-0.30980.96730.12320.09520.87640.01130.652610.687710.9146-43.6433
57.3282.84510.47484.94660.73043.08380.11190.09390.88760.25750.06510.0418-0.50380.1388-0.08280.6110.15920.08710.5001-0.00360.8937-15.317927.044-73.5315
67.28992.47743.33262.03886.84027.3411-0.01120.04290.047-0.2933-0.03570.44421.4234-0.41450.24541.26410.09590.17110.7210.13930.6816-40.17691.9423-83.9871
76.15791.35451.9494.72611.41896.3502-0.33380.51380.0026-0.74970.1942-0.11090.66710.15420.04430.7770.17090.15040.54690.07310.6067-3.704114.9972-85.3766
82.9323-1.9129-2.03676.53915.07265.18290.03750.79590.2201-0.41560.1101-0.0868-0.2789-1.0039-0.16421.4256-0.08630.08520.97510.05180.59-31.73281.276-99.6112
92.156-0.51761.78842.2905-1.82082.38990.7929-0.4918-0.21890.7233-0.39192.6479-0.4485-1.9391-0.34960.8390.13330.13191.0368-0.15671.2606-34.6315-20.5956-64.4719
105.59073.4389-6.38626.467-4.89767.5055-1.5731-0.43711.9315-0.39580.07680.3915-1.58731.71830.2870.6367-0.2934-0.26551.15250.20471.76596.592938.7679-75.0498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:114 )H1 - 114
2X-RAY DIFFRACTION2( CHAIN H AND RESID 115:213 )H115 - 213
3X-RAY DIFFRACTION3( CHAIN L AND RESID 2:109 )L2 - 109
4X-RAY DIFFRACTION4( CHAIN L AND RESID 110:209 )L110 - 209
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1:114 )A1 - 114
6X-RAY DIFFRACTION6( CHAIN A AND RESID 115:210 )A115 - 210
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:109 )B3 - 109
8X-RAY DIFFRACTION8( CHAIN B AND RESID 110:209 )B110 - 209
9X-RAY DIFFRACTION9( CHAIN P AND RESID 668:684 )P668 - 684
10X-RAY DIFFRACTION10( CHAIN Q AND RESID 669:684 )Q669 - 684

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