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- PDB-6uce: N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusi... -

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Basic information

Entry
Database: PDB / ID: 6uce
TitleN123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
Components
  • HIV fusion peptide
  • N123-VRC34_pI3 heavy chain
  • N123-VRC34_pI3 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / neutralizing / antibody / fusion peptide / IMMUNE SYSTEM-VIRAL PROTEIN complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / 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 / immune response / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.382 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: Cell Host Microbe / Year: 2020
Title: VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage.
Authors: Shen, C.H. / DeKosky, B.J. / Guo, Y. / Xu, K. / Gu, Y. / Kilam, D. / Ko, S.H. / Kong, R. / Liu, K. / Louder, M.K. / Ou, L. / Zhang, B. / Chao, C.W. / Corcoran, M.M. / Feng, E. / Huang, J. / ...Authors: Shen, C.H. / DeKosky, B.J. / Guo, Y. / Xu, K. / Gu, Y. / Kilam, D. / Ko, S.H. / Kong, R. / Liu, K. / Louder, M.K. / Ou, L. / Zhang, B. / Chao, C.W. / Corcoran, M.M. / Feng, E. / Huang, J. / Normandin, E. / O'Dell, S. / Ransier, A. / Rawi, R. / Sastry, M. / Schmidt, S.D. / Wang, S. / Wang, Y. / Chuang, G.Y. / Doria-Rose, N.A. / Lin, B. / Zhou, T. / Boritz, E.A. / Connors, M. / Douek, D.C. / Karlsson Hedestam, G.B. / Sheng, Z. / Shapiro, L. / Mascola, J.R. / Kwong, P.D.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
L: N123-VRC34_pI3 light chain
H: N123-VRC34_pI3 heavy chain
C: HIV fusion peptide


Theoretical massNumber of molelcules
Total (without water)49,0293
Polymers49,0293
Non-polymers00
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-38 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.807, 80.727, 69.819
Angle α, β, γ (deg.)90.000, 102.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody N123-VRC34_pI3 light chain


Mass: 23342.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6GMX0
#2: Protein N123-VRC34_pI3 heavy chain


Mass: 24953.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide


Mass: 732.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.175 M sodium chloride, 19.5% PEG3350

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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: Jul 1, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 89502 / % possible obs: 94.5 % / Redundancy: 3 % / Biso Wilson estimate: 15.11 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.044 / Rrim(I) all: 0.076 / Χ2: 2.179 / Net I/σ(I): 13.7 / Num. measured all: 267907
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.38-1.42.90.27539310.8940.190.3360.66184.3
1.4-1.4330.24645920.9160.1680.2990.72196.9
1.43-1.463.10.23645630.9070.160.2870.78497.2
1.46-1.493.10.21246210.9290.1420.2560.88897.5
1.49-1.523.10.19146200.9410.1290.2310.97997.6
1.52-1.553.10.17345740.9430.1190.2111.05597.5
1.55-1.5930.16445720.9380.1130.21.24696.6
1.59-1.642.90.14645520.9490.1030.1791.40796.2
1.64-1.682.70.13643430.9530.1010.171.61192.5
1.68-1.743.10.12645650.9680.0860.1541.85396
1.74-1.83.20.11145740.9760.0750.1352.0497.1
1.8-1.873.20.09946040.9790.0670.122.40296.8
1.87-1.963.10.0945450.9830.0610.1092.82295.9
1.96-2.0630.07745320.9880.0530.0943.11495.8
2.06-2.192.90.0744330.9880.050.0873.45294.1
2.19-2.362.60.06542640.9870.0490.0823.78289.4
2.36-2.63.10.06245110.9910.0430.0763.87795
2.6-2.9730.05645320.9910.0390.0683.95595.2
2.97-3.752.90.0543670.9930.0350.0614.05691.8
3.75-502.70.04642070.9920.0340.0573.71186.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.382→31.417 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 4485 5.01 %
Rwork0.1802 84961 -
obs0.1814 89446 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.37 Å2 / Biso mean: 25.144 Å2 / Biso min: 8.21 Å2
Refinement stepCycle: final / Resolution: 1.382→31.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 0 735 4147
Biso mean---34.56 -
Num. residues----450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3824-1.39820.22611270.2265241182
1.3982-1.41460.23071440.2129287296
1.4146-1.43190.24841310.21293197
1.4319-1.450.23381470.2122288597
1.45-1.46910.23451460.2025293198
1.4691-1.48920.24151690.1985289897
1.4892-1.51050.20291470.1936289498
1.5105-1.5330.22081550.1981293298
1.533-1.5570.19731630.1916291197
1.557-1.58250.21011460.189289797
1.5825-1.60980.2111680.1848286096
1.6098-1.6390.20351370.1804287796
1.639-1.67060.23011460.1882277793
1.6706-1.70470.21281590.1981275792
1.7047-1.74170.24571420.1963291197
1.7417-1.78220.18691440.1917295897
1.7822-1.82680.23421590.1946286097
1.8268-1.87620.21531490.1936289996
1.8762-1.93140.20791520.1983287296
1.9314-1.99370.20911690.1908285096
1.9937-2.0650.20761450.1855287796
2.065-2.14760.20651590.1824282394
2.1476-2.24530.22811550.1787279193
2.2453-2.36370.16421390.1807262388
2.3637-2.51170.20671500.1821284295
2.5117-2.70550.21631420.1848289496
2.7055-2.97760.23271460.181284795
2.9776-3.4080.1911520.1711276292
3.408-4.2920.16921560.1514263187
4.292-31.410.19181410.1661268888

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