[English] 日本語
Yorodumi
- PDB-3ifo: X-ray structure of amyloid beta peptide:antibody (Abeta1-7:10D5) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ifo
TitleX-ray structure of amyloid beta peptide:antibody (Abeta1-7:10D5) complex
Components
  • 10D5 FAB antibody heavy chain
  • 10D5 FAB antibody light chain
  • Amyloid beta A4 protein
KeywordsIMMUNE SYSTEM / antibody / amyloid beta peptide
Function / homology
Function and homology information


regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / positive regulation of DNA-binding transcription factor activity / G2/M transition of mitotic cell cycle / cell-cell junction / synaptic vesicle / positive regulation of tumor necrosis factor production / regulation of translation
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWeis, W.I. / Feinberg, H. / Basi, G.S. / Schenk, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural correlates of antibodies associated with acute reversal of amyloid beta-related behavioral deficits in a mouse model of Alzheimer disease.
Authors: Basi, G.S. / Feinberg, H. / Oshidari, F. / Anderson, J. / Barbour, R. / Baker, J. / Comery, T.A. / Diep, L. / Gill, D. / Johnson-Wood, K. / Goel, A. / Grantcharova, K. / Lee, M. / Li, J. / ...Authors: Basi, G.S. / Feinberg, H. / Oshidari, F. / Anderson, J. / Barbour, R. / Baker, J. / Comery, T.A. / Diep, L. / Gill, D. / Johnson-Wood, K. / Goel, A. / Grantcharova, K. / Lee, M. / Li, J. / Partridge, A. / Griswold-Prenner, I. / Piot, N. / Walker, D. / Widom, A. / Pangalos, M.N. / Seubert, P. / Jacobsen, J.S. / Schenk, D. / Weis, W.I.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 25, 2013Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: 10D5 FAB antibody heavy chain
L: 10D5 FAB antibody light chain
P: Amyloid beta A4 protein
A: 10D5 FAB antibody heavy chain
B: 10D5 FAB antibody light chain
Q: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)98,7346
Polymers98,7346
Non-polymers00
Water15,169842
1
H: 10D5 FAB antibody heavy chain
L: 10D5 FAB antibody light chain
P: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)49,3673
Polymers49,3673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-25 kcal/mol
Surface area19550 Å2
MethodPISA
2
A: 10D5 FAB antibody heavy chain
B: 10D5 FAB antibody light chain
Q: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)49,3673
Polymers49,3673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.31, 99.97, 103.96
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody 10D5 FAB antibody heavy chain


Mass: 24260.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: CET1018 / Cell line (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARY
#2: Antibody 10D5 FAB antibody light chain


Mass: 24215.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: CET1018 / Cell line (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): OVARY
#3: Protein/peptide Amyloid beta A4 protein


Mass: 890.897 Da / Num. of mol.: 2 / Fragment: residues 672-678 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 842 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 15 mg/ml, 10 mM Hepes pH 7.5, 75 mM NaCl. Protein:peptide molar ratio: 1:2. Reservoir: 30% PEG4K, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.07 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.15→43.383 Å / Num. obs: 54491 / Rmerge(I) obs: 0.058

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.383 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.29 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2752 5.06 %
Rwork0.1623 --
obs0.1651 54421 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.07 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 131.69 Å2 / Biso mean: 33.025 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.244 Å20 Å2-0 Å2
2--1.456 Å20 Å2
3----0.212 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6782 0 0 842 7624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087018
X-RAY DIFFRACTIONf_angle_d1.1679566
X-RAY DIFFRACTIONf_chiral_restr0.0811099
X-RAY DIFFRACTIONf_plane_restr0.0051212
X-RAY DIFFRACTIONf_dihedral_angle_d16.6252518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18710.23781430.14972209X-RAY DIFFRACTION86
2.1871-2.22690.2091050.15252384X-RAY DIFFRACTION92
2.2269-2.26970.23241120.1622479X-RAY DIFFRACTION95
2.2697-2.3160.27421390.16542563X-RAY DIFFRACTION98
2.316-2.36640.2221230.1692574X-RAY DIFFRACTION100
2.3664-2.42140.25661520.17182577X-RAY DIFFRACTION100
2.4214-2.4820.24061360.17332629X-RAY DIFFRACTION100
2.482-2.54910.25131300.17962596X-RAY DIFFRACTION100
2.5491-2.62410.27031570.17532593X-RAY DIFFRACTION100
2.6241-2.70880.24971380.17582584X-RAY DIFFRACTION100
2.7088-2.80560.27351380.18552611X-RAY DIFFRACTION100
2.8056-2.91790.23621490.16982596X-RAY DIFFRACTION100
2.9179-3.05060.22211420.17692608X-RAY DIFFRACTION100
3.0506-3.21140.21741200.17382656X-RAY DIFFRACTION100
3.2114-3.41250.22721500.17572596X-RAY DIFFRACTION100
3.4125-3.67590.21511430.15572623X-RAY DIFFRACTION100
3.6759-4.04560.18761440.14572661X-RAY DIFFRACTION100
4.0456-4.63040.17111390.11692663X-RAY DIFFRACTION100
4.6304-5.83160.15081370.11342693X-RAY DIFFRACTION100
5.8316-43.39210.17861550.15252774X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72050.04640.46520.62410.07131.5101-0.0230.05450.0681-0.0879-0.0102-0.0548-0.10630.09340.030.0938-0.02950.00070.09710.00740.1016-20.197518.256725.7428
21.204-0.25440.3531.69850.41960.64070.01380.04960.0431-0.0682-0.0201-0.1882-0.05820.09040.00110.1181-0.00780.030.13910.01840.10050.52370.180949.0066
31.0947-0.8131-0.00830.44570.61020.35490.26010.02250.2813-0.23450.0534-0.03270.0526-0.0698-0.19120.2698-0.0090.02420.15210.04580.1777-23.508626.266512.366
41.1885-0.00150.44461.0040.2740.64030.0549-0.021-0.08530.0427-0.02830.0188-0.0334-0.0212-0.01470.0898-0.022-0.00710.1160.02710.07570.5472-1.2192-9.0514
50.6071-0.5811-0.56842.53280.71961.2153-0.1748-0.18090.07870.68830.1481-0.20390.27590.03820.02950.29080.0355-0.06350.1572-0.00510.144812.984416.210619.8975
6-0.93680.4443-0.29510.69360.8163.1338-0.30.356-0.29270.0679-0.06830.20530.04090.03760.25610.0983-0.02160.00240.2557-0.00480.174-10.5403-9.4044-17.0008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1-123) or (chain L and resid 1-112)H1 - 123
2X-RAY DIFFRACTION1(chain H and resid 1-123) or (chain L and resid 1-112)L1 - 112
3X-RAY DIFFRACTION2(chain H and resid 124-225) or (chain L and resid 113-219)H124 - 225
4X-RAY DIFFRACTION2(chain H and resid 124-225) or (chain L and resid 113-219)L113 - 219
5X-RAY DIFFRACTION3chain P and resid 1-7P1 - 7
6X-RAY DIFFRACTION4(chain A and resid 1-123) or (chain B and resid 1-112)A1 - 123
7X-RAY DIFFRACTION4(chain A and resid 1-123) or (chain B and resid 1-112)B1 - 112
8X-RAY DIFFRACTION5(chain A and resid 124-225) or (chain B and resid 113-219)A124 - 225
9X-RAY DIFFRACTION5(chain A and resid 124-225) or (chain B and resid 113-219)B113 - 219
10X-RAY DIFFRACTION6chain Q and resid 1-7Q1 - 7

+
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