[English] 日本語
Yorodumi
- PDB-7ekk: Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ekk
TitleAnti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide
Components
  • Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
  • Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
  • MPER region of the envelope glycoprotein gp41 from HIV-1
KeywordsIMMUNE SYSTEM / IgG / Fab / Chemical modification
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / AMMONIUM ION
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Nieva, J.L.
CitationJournal: Iscience / Year: 2021
Title: Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile.
Authors: Rujas, E. / Leaman, D.P. / Insausti, S. / Carravilla, P. / Garcia-Porras, M. / Largo, E. / Morillo, I. / Sanchez-Eugenia, R. / Zhang, L. / Cui, H. / Iloro, I. / Elortza, F. / Julien, J.P. / ...Authors: Rujas, E. / Leaman, D.P. / Insausti, S. / Carravilla, P. / Garcia-Porras, M. / Largo, E. / Morillo, I. / Sanchez-Eugenia, R. / Zhang, L. / Cui, H. / Iloro, I. / Elortza, F. / Julien, J.P. / Eggeling, C. / Zwick, M.B. / Caaveiro, J.M.M. / Nieva, J.L.
History
DepositionApr 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
L: Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide
P: MPER region of the envelope glycoprotein gp41 from HIV-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16210
Polymers48,6443
Non-polymers5187
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-55 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.981, 44.800, 85.949
Angle α, β, γ (deg.)90.000, 113.630, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MPER region of the envelope glycoprotein gp41 from HIV-1


Mass: 2187.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

-
Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide


Mass: 23350.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: immunoglobin / Production host: Escherichia coli BL21 (bacteria)
#2: Antibody Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide


Mass: 23106.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: immunoglobulin / Production host: Escherichia coli BL21 (bacteria)

-
Non-polymers , 5 types, 509 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.06 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4,000 30% Ammonium sulphate 200 mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.7→34.4 Å / Num. obs: 57219 / % possible obs: 94.2 % / Redundancy: 2.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.8
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6629 / CC1/2: 0.77

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CIN

5cin


Resolution: 1.7→34.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.876 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 2324 4.1 %RANDOM
Rwork0.1584 ---
obs0.1597 54867 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.58 Å2 / Biso mean: 16.977 Å2 / Biso min: 7.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.34 Å2
2---1.11 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.7→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 31 504 3901
Biso mean--26.63 28.57 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133588
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173252
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6464907
X-RAY DIFFRACTIONr_angle_other_deg1.4261.5717603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.8945.421499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03722.089158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85315552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 126 -
Rwork0.258 2869 -
all-2995 -
obs--67.44 %

+
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