[English] 日本語
Yorodumi
- PDB-3lex: 2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lex
Title2F5 Epitope scaffold elicited anti-HIV-1 monoclonal antibody 11F10 in complex with HIV-1 GP41
Components
  • 11f10 Antibody Heavy Chain
  • 11f10 Antibody Light Chain
  • Envelope glycoprotein gp41
KeywordsIMMUNE SYSTEM / HIV-1 / GP-41 / MONOCLONAL ANTIBODY / 2F5 / SCAFFOLD / EPITOPE / TRANSPLANT / GRAFT / RE-ELCITATION / Envelope protein / VACCINE DESIGN
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsOfek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Elicitation of structure-specific antibodies by epitope scaffolds.
Authors: Ofek, G. / Guenaga, F.J. / Schief, W.R. / Skinner, J. / Baker, D. / Wyatt, R. / Kwong, P.D.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_sheet.number_strands
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 11f10 Antibody Heavy Chain
L: 11f10 Antibody Light Chain
P: Envelope glycoprotein gp41
A: 11f10 Antibody Heavy Chain
B: 11f10 Antibody Light Chain
C: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)98,3346
Polymers98,3346
Non-polymers00
Water11,313628
1
H: 11f10 Antibody Heavy Chain
L: 11f10 Antibody Light Chain
P: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,1673
Polymers49,1673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-30 kcal/mol
Surface area18830 Å2
MethodPISA
2
A: 11f10 Antibody Heavy Chain
B: 11f10 Antibody Light Chain
C: Envelope glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)49,1673
Polymers49,1673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-31 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.543, 70.962, 78.265
Angle α, β, γ (deg.)90.08, 90.02, 90.29
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody 11f10 Antibody Heavy Chain


Mass: 23916.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#2: Antibody 11f10 Antibody Light Chain


Mass: 24264.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma / Cell line: myeloma cell line FO / Strain: BALB/c
#3: Protein/peptide Envelope glycoprotein gp41


Mass: 986.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: HIV-1 gp41 peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9IJQ0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 4000, 0.08 M CH3COONA, 0.04 M, TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2009
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→25.9 Å / Num. obs: 49925 / % possible obs: 94.6 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 19.46 Å2 / Rsym value: 0.038 / Net I/σ(I): 33
Reflection shellResolution: 1.97→2.04 Å / Mean I/σ(I) obs: 12.9 / Rsym value: 0.092 / % possible all: 94.7

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LEY

3ley


Resolution: 1.97→25.9 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.16 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1992 4.03 %
Rwork0.165 --
obs0.166 49480 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.85 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1-11.486 Å21.457 Å2-2.512 Å2
2---10.321 Å20.631 Å2
3----1.165 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6783 0 0 628 7411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096967
X-RAY DIFFRACTIONf_angle_d0.8929496
X-RAY DIFFRACTIONf_dihedral_angle_d14.1742419
X-RAY DIFFRACTIONf_chiral_restr0.061074
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.965-2.0140.2491260.1853168X-RAY DIFFRACTION86
2.014-2.0690.2351430.1733431X-RAY DIFFRACTION94
2.069-2.1290.2251450.1763416X-RAY DIFFRACTION94
2.129-2.1980.2471420.1663434X-RAY DIFFRACTION95
2.198-2.2770.2521350.1833429X-RAY DIFFRACTION95
2.277-2.3680.2251460.1813473X-RAY DIFFRACTION95
2.368-2.4750.2381470.1843486X-RAY DIFFRACTION95
2.475-2.6060.2561450.1773433X-RAY DIFFRACTION95
2.606-2.7690.2071400.183414X-RAY DIFFRACTION94
2.769-2.9820.2221470.1733413X-RAY DIFFRACTION95
2.982-3.2820.191400.1623399X-RAY DIFFRACTION93
3.282-3.7560.1651390.1453362X-RAY DIFFRACTION92
3.756-4.7270.1471450.1343327X-RAY DIFFRACTION92
4.727-25.9030.1541520.1673303X-RAY DIFFRACTION91

+
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