[English] 日本語
Yorodumi
- PDB-5tkk: Structure of mouse vaccination-elicited HIV neutralizing antibody... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tkk
TitleStructure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex with HIV-1 fusion peptide residue 512-519
Components
  • HIV-1 fusion peptide residue 512-519
  • mouse antibody vFP5.01 heavy chain
  • mouse antibody vFP5.01 light chain
KeywordsIMMUNE SYSTEM / Neutralizing / mouse / antibody / fusion-peptide / complex
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 / 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 / host cell plasma membrane / structural molecule activity / virion membrane / 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 speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsXu, K. / Liu, K. / Kwong, P.D.
CitationJournal: Nat Med / Year: 2018
Title: Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.
Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou ...Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Mangaiarkarasi Asokan / Robert T Bailer / Michael Chambers / Xuejun Chen / Chang W Choi / Venkata P Dandey / Nicole A Doria-Rose / Aliaksandr Druz / Edward T Eng / S Katie Farney / Kathryn E Foulds / Hui Geng / Ivelin S Georgiev / Jason Gorman / Kurt R Hill / Alexander J Jafari / Young D Kwon / Yen-Ting Lai / Thomas Lemmin / Krisha McKee / Tiffany Y Ohr / Li Ou / Dongjun Peng / Ariana P Rowshan / Zizhang Sheng / John-Paul Todd / Yaroslav Tsybovsky / Elise G Viox / Yiran Wang / Hui Wei / Yongping Yang / Amy F Zhou / Rui Chen / Lu Yang / Diana G Scorpio / Adrian B McDermott / Lawrence Shapiro / Bridget Carragher / Clinton S Potter / John R Mascola / Peter D Kwong /
Abstract: A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N- ...A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 fusion peptide residue 512-519
H: mouse antibody vFP5.01 heavy chain
L: mouse antibody vFP5.01 light chain


Theoretical massNumber of molelcules
Total (without water)48,7893
Polymers48,7893
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-34 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.237, 82.233, 72.264
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide HIV-1 fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Antibody mouse antibody vFP5.01 heavy chain


Mass: 24360.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody mouse antibody vFP5.01 light chain


Mass: 23696.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Tris-HCl pH8.5, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid N3
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25.469 Å / Num. obs: 59733 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Χ2: 1.054 / Net I/av σ(I): 16.148 / Net I/σ(I): 13.1 / Num. measured all: 209617
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.55-1.582.10.4680.763177.3
1.58-1.612.30.4960.759193.7
1.61-1.642.80.5270.761197.2
1.64-1.673.20.530.79198.1
1.67-1.713.40.5120.821198.3
1.71-1.753.60.4320.893198.5
1.75-1.793.60.3380.931198.5
1.79-1.843.60.2650.951198.6
1.84-1.893.60.2020.966198.8
1.89-1.953.70.1570.979199.1
1.95-2.023.80.1350.981199.1
2.02-2.13.80.1150.987199.3
2.1-2.23.80.1010.987199.4
2.2-2.323.80.090.989199.5
2.32-2.463.80.0830.99199.6
2.46-2.653.80.0740.992199.8
2.65-2.923.80.0670.993199.9
2.92-3.343.80.0560.995199.8
3.34-4.213.70.0470.996199.4
4.21-503.50.0380.997191.8

-
Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.469 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.31
RfactorNum. reflection% reflection
Rfree0.2469 2929 4.91 %
Rwork0.209 --
obs0.2109 59675 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.72 Å2 / Biso mean: 37.5113 Å2 / Biso min: 9.87 Å2
Refinement stepCycle: final / Resolution: 1.55→25.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 337 3693
Biso mean---42.34 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013439
X-RAY DIFFRACTIONf_angle_d1.2754683
X-RAY DIFFRACTIONf_chiral_restr0.077526
X-RAY DIFFRACTIONf_plane_restr0.008594
X-RAY DIFFRACTIONf_dihedral_angle_d17.3842052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.57550.42771250.31312127225277
1.5755-1.60270.36551190.3062572269193
1.6027-1.63180.33841210.29482663278497
1.6318-1.66320.32581640.2862696286098
1.6632-1.69720.32271350.28042728286398
1.6972-1.73410.29941530.27422724287798
1.7341-1.77440.29511300.2642722285298
1.7744-1.81870.2981300.27182755288599
1.8187-1.86790.30131550.2582720287599
1.8679-1.92290.35521370.25282764290199
1.9229-1.98490.23741270.232714284199
1.9849-2.05580.29651640.23082757292199
2.0558-2.13810.24761610.22162767292899
2.1381-2.23530.26081210.23282760288199
2.2353-2.35310.26241610.2342711287299
2.3531-2.50040.26441330.226827982931100
2.5004-2.69330.25541460.226427742920100
2.6933-2.96390.24821420.208727992941100
2.9639-3.3920.23051580.192227562914100
3.392-4.27030.1911380.16212810294899
4.2703-25.47280.19581090.15892629273892
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)
10.0182-0.03540.00040.1172-0.00390.00030.0146-0.02650.01470.02380.01030.0042-0.03340.02610.02170.72320.05790.14650.62370.00690.240636.9558-7.660442.5224
20.35810.0715-0.39720.4547-0.13950.41230.0691-0.2113-0.06550.01570.0832-0.01280.0443-0.40340.29850.2195-0.0832-0.02270.41860.00640.128541.4641-21.298133.0662
30.39720.2819-0.44190.34270.00241.3445-0.0913-0.2083-0.02090.0974-0.1767-0.1430.32950.2657-0.35120.1351-0.0362-0.02380.11150.04990.221958.0069-21.30014.1415
40.02990.0234-0.06630.0264-0.07230.19670.1135-0.1654-0.08180.010.05430.1197-0.0024-0.13850.0080.44050.26410.16610.79420.29790.47229.9794-4.645918.8133
50.1212-0.0073-0.10080.0233-0.01660.20710.0076-0.0840.0451-0.07750.1059-0.0544-0.1392-0.06580.26610.78560.31440.4120.49360.19320.668634.31625.222418.7261
60.15110.00270.12970.10830.00750.11260.2708-0.11960.31040.33780.04470.2096-0.38760.05560.43020.6420.03420.26050.3697-0.04410.300839.6425-1.362629.1331
70.0992-0.0327-0.16190.3356-0.14520.43650.0792-0.04510.26950.09790.30130.2123-0.2989-0.07060.40610.68510.15790.30250.42770.07150.480637.38692.095523.3716
80.16650.1576-0.22250.1353-0.29051.08410.0038-0.0437-0.05340.02270.09660.0549-0.0697-0.44550.35690.2040.09460.04080.09170.03950.195645.7693-11.69564.683
90.01010.00970.00790.00890.00840.12050.00270.0682-0.0676-0.11540.06360.0460.0712-0.0980.04810.2262-0.0877-0.05470.5168-0.02230.163142.7372-18.6253-13.8477
100.0365-0.0998-0.19320.57260.40751.17140.0490.13080.04470.14950.0649-0.0269-0.2437-0.3330.16430.17-0.0003-0.0090.1513-0.02040.202646.0441-10.1242.9112
110.75570.0689-0.54360.37640.19380.5663-0.03820.46130.0807-0.2801-0.02330.0280.0848-0.52060.02620.2292-0.0529-0.04380.2553-0.04960.158248.7755-18.5823-13.165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 512 through 519 )A512 - 519
2X-RAY DIFFRACTION2chain 'H' and (resid 2 through 109 )H2 - 109
3X-RAY DIFFRACTION3chain 'H' and (resid 110 through 215 )H110 - 215
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 13 )L1 - 13
5X-RAY DIFFRACTION5chain 'L' and (resid 14 through 25 )L14 - 25
6X-RAY DIFFRACTION6chain 'L' and (resid 26 through 61 )L26 - 61
7X-RAY DIFFRACTION7chain 'L' and (resid 62 through 90 )L62 - 90
8X-RAY DIFFRACTION8chain 'L' and (resid 91 through 144 )L91 - 144
9X-RAY DIFFRACTION9chain 'L' and (resid 145 through 155 )L145 - 155
10X-RAY DIFFRACTION10chain 'L' and (resid 156 through 174 )L156 - 174
11X-RAY DIFFRACTION11chain 'L' and (resid 175 through 213 )L175 - 213

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more