[English] 日本語
Yorodumi
- PDB-1cu4: CRYSTAL STRUCTURE OF THE ANTI-PRION FAB 3F4 IN COMPLEX WITH ITS P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cu4
TitleCRYSTAL STRUCTURE OF THE ANTI-PRION FAB 3F4 IN COMPLEX WITH ITS PEPTIDE EPITOPE
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
  • RECOGNITION PEPTIDE
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsKanyo, Z.F. / Pan, K.M. / Williamson, R.A. / Burton, D.R. / Prusiner, S.B. / Fletterick, R.J. / Cohen, F.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Antibody binding defines a structure for an epitope that participates in the PrPC-->PrPSc conformational change.
Authors: Kanyo, Z.F. / Pan, K.M. / Williamson, R.A. / Burton, D.R. / Prusiner, S.B. / Fletterick, R.J. / Cohen, F.E.
History
DepositionAug 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: FAB LIGHT CHAIN
H: FAB HEAVY CHAIN
P: RECOGNITION PEPTIDE


Theoretical massNumber of molelcules
Total (without water)48,5553
Polymers48,5553
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-31 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.470, 77.350, 134.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Antibody FAB LIGHT CHAIN / ANTI-PRION FAB 3F4


Mass: 24080.775 Da / Num. of mol.: 1 / Fragment: FAB ANTIBODY 3F4, LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB HEAVY CHAIN / ANTI-PRION FAB 3F4


Mass: 23342.943 Da / Num. of mol.: 1 / Fragment: FAB ANTIBODY 3F4, HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide RECOGNITION PEPTIDE


Mass: 1131.390 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence cooresponding to aa104-113 of Syrian hamster prion protein
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlpeptide1drop
210 mMTris-HCl1drop
320 mM imidazole1drop
412 %PEG80001drop
522 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 28, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 8689 / Num. obs: 8689 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.5
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.216 / % possible all: 90.4
Reflection shell
*PLUS
% possible obs: 90.4 % / Num. unique obs: 1011

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 839 random
Rwork0.159 --
all-8662 -
obs-8040 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 9 3403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.681

+
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://pdbjlvh1.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