[English] 日本語
Yorodumi
- PDB-6pef: Vaccine-elicited NHP FP-targeting antibody DF2F-a.01 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pef
TitleVaccine-elicited NHP FP-targeting antibody DF2F-a.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV fusion peptide residue 512-519
  • antibody DF2F-a.01 heavy chain
  • antibody DF2F-a.01 light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / NHP / FP / Fusion Peptide / vaccine
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 / virus-mediated perturbation of host defense response / host cell endosome membrane ...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 / virus-mediated perturbation of host defense response / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsXu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: To Be Published
Title: Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies
Authors: Xu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: antibody DF2F-a.01 heavy chain
B: antibody DF2F-a.01 light chain
C: HIV fusion peptide residue 512-519
D: antibody DF2F-a.01 heavy chain
E: antibody DF2F-a.01 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)94,3396
Polymers94,3396
Non-polymers00
Water12,538696
1
A: antibody DF2F-a.01 heavy chain
B: antibody DF2F-a.01 light chain
C: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,1703
Polymers47,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-36 kcal/mol
Surface area19310 Å2
MethodPISA
2
D: antibody DF2F-a.01 heavy chain
E: antibody DF2F-a.01 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,1703
Polymers47,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-36 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.574, 52.504, 151.716
Angle α, β, γ (deg.)90.000, 90.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12(chain B and resid 3 through 212)
22chain E
13chain C
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA2 - 220
211chain DD2 - 220
112(chain B and resid 3 through 212)B3 - 212
212chain EE3 - 212
113chain CC512 - 519
213chain FF512 - 519

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody antibody DF2F-a.01 heavy chain


Mass: 23785.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody antibody DF2F-a.01 light chain


Mass: 22651.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350

-
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: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 75515 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.068 / Rrim(I) all: 0.131 / Χ2: 1.274 / Net I/σ(I): 8.6 / Num. measured all: 263243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.60.66536620.5750.4730.820.75696.1
2.03-2.072.80.64836720.5980.4450.7890.91696.5
2.07-2.1130.60937300.6820.4050.7340.89197.1
2.11-2.153.20.51436790.7410.3320.6140.87996.8
2.15-2.23.30.46637370.8010.2950.5530.92897.3
2.2-2.253.40.46237410.8050.2880.5461.11197.4
2.25-2.313.60.42137140.8640.2590.4951.02697.4
2.31-2.373.60.34937580.8860.2130.411.08297.6
2.37-2.443.60.30537270.9160.1850.3581.15397.7
2.44-2.523.60.25337560.9530.1540.2971.18697.9
2.52-2.613.70.21838060.9540.1320.2551.37798.1
2.61-2.713.60.18937580.9650.1150.2221.49598.2
2.71-2.843.70.16237600.9690.0980.1891.698.3
2.84-2.993.70.13838070.9730.0840.1621.798.4
2.99-3.173.70.12238100.9750.0740.1421.64198.8
3.17-3.423.70.10638270.9820.0640.1241.69598.8
3.42-3.763.70.08938420.9880.0530.1041.62398.9
3.76-4.313.70.07438560.990.0450.0871.37199.1
4.31-5.433.70.05738800.9920.0340.0671.25599.4
5.43-503.60.05539930.9940.0340.0651.14898.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→43.171 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2136 3552 4.71 %
Rwork0.183 --
obs0.1845 75461 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.97 Å2 / Biso mean: 37.1861 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 2.004→43.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 0 696 7162
Biso mean---43.54 -
Num. residues----875
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1320X-RAY DIFFRACTION2.269TORSIONAL
12D1320X-RAY DIFFRACTION2.269TORSIONAL
21B1260X-RAY DIFFRACTION2.269TORSIONAL
22E1260X-RAY DIFFRACTION2.269TORSIONAL
31C42X-RAY DIFFRACTION2.269TORSIONAL
32F42X-RAY DIFFRACTION2.269TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0036-2.0310.31781150.25132573268887
2.031-2.060.25921320.24172787291996
2.06-2.09080.27641410.23772873301497
2.0908-2.12350.29691270.23812800292797
2.1235-2.15830.33021400.22432824296497
2.1583-2.19550.26991330.21542912304597
2.1955-2.23540.27721580.21512799295797
2.2354-2.27840.24531240.21832892301697
2.2784-2.32490.23291490.21032804295397
2.3249-2.37550.27681290.21442897302698
2.3755-2.43070.22261460.21592862300898
2.4307-2.49150.24961430.20452890303398
2.4915-2.55880.30471620.20722819298198
2.5588-2.63410.26531350.20282912304798
2.6341-2.71910.25331530.20442881303498
2.7191-2.81630.24121520.18982856300898
2.8163-2.9290.20841470.19132907305498
2.929-3.06230.24941310.18892926305799
3.0623-3.22370.24911500.18612884303499
3.2237-3.42560.2121400.18312935307599
3.4256-3.690.20351220.17192963308599
3.69-4.06110.14951430.15952969311299
4.0611-4.64810.16621650.13662914307999
4.6481-5.85380.16021570.14652996315399
5.8538-43.18090.18281580.17613034319298

+
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://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