[English] 日本語
Yorodumi
- PDB-5jny: Crystal Structure of 10E8 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jny
TitleCrystal Structure of 10E8 Fab
Components
  • 10E8 Heavy Chain
  • 10E8 Light Chain
KeywordsIMMUNE SYSTEM / MPER / HIV / antibody / neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ISOPROPYL ALCOHOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.041 Å
AuthorsOfek, G. / Kwong, P.
CitationJournal: Plos One / Year: 2016
Title: Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8.
Authors: Soto, C. / Ofek, G. / Joyce, M.G. / Zhang, B. / McKee, K. / Longo, N.S. / Yang, Y. / Huang, J. / Parks, R. / Eudailey, J. / Lloyd, K.E. / Alam, S.M. / Haynes, B.F. / Mullikin, J.C. / ...Authors: Soto, C. / Ofek, G. / Joyce, M.G. / Zhang, B. / McKee, K. / Longo, N.S. / Yang, Y. / Huang, J. / Parks, R. / Eudailey, J. / Lloyd, K.E. / Alam, S.M. / Haynes, B.F. / Mullikin, J.C. / Connors, M. / Mascola, J.R. / Shapiro, L. / Kwong, P.D.
History
DepositionMay 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 10E8 Heavy Chain
B: 10E8 Light Chain
C: 10E8 Heavy Chain
D: 10E8 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5977
Polymers96,4414
Non-polymers1563
Water30617
1
A: 10E8 Heavy Chain
B: 10E8 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2813
Polymers48,2212
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-10 kcal/mol
Surface area21040 Å2
MethodPISA
2
C: 10E8 Heavy Chain
D: 10E8 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3164
Polymers48,2212
Non-polymers962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-30 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.627, 248.627, 54.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Antibody 10E8 Heavy Chain


Mass: 25318.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 10E8 Light Chain


Mass: 22902.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 5.02 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% PEG 8000, 25% Isopropanol, 0.1 M Imidazole pH 6.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 37419 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.07 / Rrim(I) all: 0.232 / Χ2: 0.964 / Net I/av σ(I): 10.4 / Net I/σ(I): 3.5 / Num. measured all: 397174
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.05-3.167.60.684198.3
3.16-3.299.20.598199.7
3.29-3.4310.50.4341100
3.43-3.6211.10.3711100
3.62-3.8411.40.2991100
3.84-4.1411.40.2411100
4.14-4.5611.40.1831100
4.56-5.2111.40.1811100
5.21-6.5711.20.1851100
6.57-5010.80.094199.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6 Å32.84 Å
Translation6 Å32.84 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.041→32.836 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1873 5.01 %
Rwork0.1876 --
obs0.189 37387 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.041→32.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6767 0 9 17 6793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036967
X-RAY DIFFRACTIONf_angle_d0.7179468
X-RAY DIFFRACTIONf_dihedral_angle_d11.592478
X-RAY DIFFRACTIONf_chiral_restr0.0281036
X-RAY DIFFRACTIONf_plane_restr0.0041219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0408-3.12290.33851660.29132552X-RAY DIFFRACTION96
3.1229-3.21480.28121450.27092712X-RAY DIFFRACTION100
3.2148-3.31840.2881430.25622702X-RAY DIFFRACTION100
3.3184-3.43690.2511330.22632749X-RAY DIFFRACTION100
3.4369-3.57440.25611400.22252705X-RAY DIFFRACTION100
3.5744-3.73680.24021320.21772704X-RAY DIFFRACTION100
3.7368-3.93350.24591560.19912743X-RAY DIFFRACTION100
3.9335-4.17950.19641530.17142744X-RAY DIFFRACTION100
4.1795-4.50150.19211410.14672725X-RAY DIFFRACTION100
4.5015-4.95310.15911490.15012744X-RAY DIFFRACTION100
4.9531-5.66670.18221340.14722761X-RAY DIFFRACTION100
5.6667-7.12740.18911530.17552769X-RAY DIFFRACTION100
7.1274-32.83750.17961280.16272904X-RAY DIFFRACTION100

+
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