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- PDB-6ucf: N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusi... -

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Basic information

Entry
Database: PDB / ID: 6ucf
TitleN123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
Components
  • HIV fusion peptide
  • N123-VRC34_pI4 heavy chain
  • N123-VRC34_pI4 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: 1.29 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 1.2Oct 16, 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_pI4 light chain
H: N123-VRC34_pI4 heavy chain
A: HIV fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,5303
Polymers48,5303
Non-polymers00
Water12,232679
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-31 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.420, 86.434, 128.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody N123-VRC34_pI4 light chain


Mass: 23281.867 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_pI4 heavy chain


Mass: 24515.410 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.: 679 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.24 M ammonium acetate, 23% PEG3350, 0.1 M Tris, pH 8.4

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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: 1.289→50 Å / Num. obs: 108470 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 11.44 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Χ2: 1.561 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.29-1.315.10.62953560.8360.3050.7010.53799.9
1.31-1.345.70.61153390.860.280.6740.5599.8
1.34-1.3660.55753740.8840.2480.6110.56699.9
1.36-1.396.20.4853730.9290.210.5250.594100
1.39-1.426.10.41453770.9320.1830.4540.6499.9
1.42-1.4560.36353730.9440.1620.3990.67999.9
1.45-1.495.80.31153380.9470.1420.3430.78499.1
1.49-1.535.30.25353420.9490.1220.2820.88599
1.53-1.575.30.21553510.9640.1020.2391.03499.4
1.57-1.636.40.19453940.9790.0830.2111.133100
1.63-1.686.50.1754350.9830.0730.1851.28100
1.68-1.756.30.14354160.9870.0630.1571.48399.9
1.75-1.836.20.12253960.9890.0540.1341.79299.7
1.83-1.935.90.10154580.9910.0460.1112.12299.9
1.93-2.055.60.08453900.9930.0390.0932.39599.4
2.05-2.215.20.07353880.9930.0350.0822.57498.9
2.21-2.436.60.06955110.9960.0290.0752.8100
2.43-2.786.50.06255080.9960.0260.0672.92199.8
2.78-3.560.05255580.9970.0230.0563.09599.7
3.5-505.60.04457930.9980.020.0492.83299.1

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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: 1.29→35.108 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.16
RfactorNum. reflection% reflection
Rfree0.1823 5439 5.03 %
Rwork0.1667 --
obs0.1675 108214 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.94 Å2 / Biso mean: 16.3604 Å2 / Biso min: 5.45 Å2
Refinement stepCycle: final / Resolution: 1.29→35.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 0 679 4065
Biso mean---28.03 -
Num. residues----447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.29-1.30320.24791390.2341309590
1.3032-1.31860.22171900.21823408100
1.3186-1.33460.22581480.20573429100
1.3346-1.35150.22111660.19923438100
1.3515-1.36930.24611820.1873410100
1.3693-1.38810.20182090.18473348100
1.3881-1.40790.21241780.17723391100
1.4079-1.42890.20111790.18043483100
1.4289-1.45130.20531720.17193361100
1.4513-1.47510.17141820.17183447100
1.4751-1.50050.18881590.1682336799
1.5005-1.52780.17771660.1666341299
1.5278-1.55720.18771720.1621338199
1.5572-1.58890.17981920.1623411100
1.5889-1.62350.1771890.15263417100
1.6235-1.66130.18471890.15563451100
1.6613-1.70280.20082030.1583388100
1.7028-1.74880.19872010.1563448100
1.7488-1.80030.17641630.16333426100
1.8003-1.85840.20131770.15983454100
1.8584-1.92480.17711940.16053472100
1.9248-2.00190.17281840.15473424100
2.0019-2.0930.16361620.1589340298
2.093-2.20330.18611830.1573344899
2.2033-2.34130.18511550.16283497100
2.3413-2.52210.20192080.17073467100
2.5221-2.77580.18172000.18263503100
2.7758-3.17720.18321990.1723498100
3.1772-4.0020.16021910.1549337795
4.002-35.10.16442070.16553722100

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