[English] 日本語
Yorodumi
- PDB-8ecv: Bovine Fab 2F12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ecv
TitleBovine Fab 2F12
Components
  • 2F12 Fab Heavy chain
  • 2F12 Fab Light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoglobulin lambda constant 2
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2.
Authors: Huang, R. / Warner Jenkins, G. / Kim, Y. / Stanfield, R.L. / Singh, A. / Martinez-Yamout, M. / Kroon, G.J. / Torres, J.L. / Jackson, A.M. / Kelley, A. / Shaabani, N. / Zeng, B. / Bacica, M. ...Authors: Huang, R. / Warner Jenkins, G. / Kim, Y. / Stanfield, R.L. / Singh, A. / Martinez-Yamout, M. / Kroon, G.J. / Torres, J.L. / Jackson, A.M. / Kelley, A. / Shaabani, N. / Zeng, B. / Bacica, M. / Chen, W. / Warner, C. / Radoicic, J. / Joh, J. / Dinali Perera, K. / Sang, H. / Kim, T. / Yao, J. / Zhao, F. / Sok, D. / Burton, D.R. / Allen, J. / Harriman, W. / Mwangi, W. / Chung, D. / Teijaro, J.R. / Ward, A.B. / Dyson, H.J. / Wright, P.E. / Wilson, I.A. / Chang, K.O. / McGregor, D. / Smider, V.V.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
L: 2F12 Fab Light chain
H: 2F12 Fab Heavy chain
A: 2F12 Fab Light chain
B: 2F12 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)101,7174
Polymers101,7174
Non-polymers00
Water9,440524
1
L: 2F12 Fab Light chain
H: 2F12 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)50,8592
Polymers50,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-28 kcal/mol
Surface area21970 Å2
MethodPISA
2
A: 2F12 Fab Light chain
B: 2F12 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)50,8592
Polymers50,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.366, 73.735, 142.831
Angle α, β, γ (deg.)90.000, 91.964, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Antibody 2F12 Fab Light chain


Mass: 22527.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: P0DOY2
#2: Antibody 2F12 Fab Heavy chain


Mass: 28330.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M sodium chloride, 0.1M phosphate-citrate buffer, 20% Peg6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.81→37 Å / Num. obs: 70456 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.093 / Rrim(I) all: 0.166 / Χ2: 1.584 / Net I/av σ(I): 10.1 / Net I/σ(I): 10.1
Reflection shellResolution: 1.81→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 2 / Num. unique obs: 3942 / CC1/2: 0.401 / Rpim(I) all: 0.634 / Rrim(I) all: 1.13 / Χ2: 0.937 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6oo0

6oo0


Resolution: 1.81→36.98 Å / SU ML: 0.2421 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 3549 5.05 %
Rwork0.2192 66781 -
obs0.2213 70330 87.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.36 Å2
Refinement stepCycle: LAST / Resolution: 1.81→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 0 524 7554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00657184
X-RAY DIFFRACTIONf_angle_d0.72159800
X-RAY DIFFRACTIONf_chiral_restr0.0511138
X-RAY DIFFRACTIONf_plane_restr0.00541254
X-RAY DIFFRACTIONf_dihedral_angle_d12.82312552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.33071220.30122255X-RAY DIFFRACTION74.05
1.83-1.860.28951450.2773014X-RAY DIFFRACTION97.86
1.86-1.880.32221940.2822916X-RAY DIFFRACTION97.92
1.88-1.910.4684710.40511187X-RAY DIFFRACTION38.91
1.91-1.950.44381510.42142630X-RAY DIFFRACTION86.99
1.95-1.980.29751580.26882949X-RAY DIFFRACTION96.85
1.98-2.010.2461680.22762992X-RAY DIFFRACTION96.61
2.01-2.050.24481280.21812866X-RAY DIFFRACTION95.11
2.05-2.10.29641520.22192864X-RAY DIFFRACTION93.06
2.1-2.140.27161260.22742762X-RAY DIFFRACTION90.08
2.14-2.190.27771560.2392936X-RAY DIFFRACTION95.76
2.19-2.250.3593730.32561393X-RAY DIFFRACTION45.08
2.25-2.310.4736690.34651510X-RAY DIFFRACTION49.42
2.31-2.370.28441650.23293029X-RAY DIFFRACTION98.64
2.37-2.450.28771710.22612961X-RAY DIFFRACTION97.78
2.45-2.540.29161750.22542972X-RAY DIFFRACTION97.46
2.54-2.640.2671740.21782939X-RAY DIFFRACTION95.55
2.64-2.760.26051740.21532870X-RAY DIFFRACTION95.3
2.76-2.910.24091530.21272942X-RAY DIFFRACTION95.73
2.91-3.090.25591180.21122760X-RAY DIFFRACTION88.74
3.09-3.330.24571440.20272982X-RAY DIFFRACTION96.81
3.33-3.660.25291120.19272431X-RAY DIFFRACTION78.01
3.66-4.190.20771510.1752637X-RAY DIFFRACTION85.34
4.19-5.270.20471480.15263046X-RAY DIFFRACTION97.05
5.28-36.980.18881510.19792938X-RAY DIFFRACTION93.07

+
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