[English] 日本語
Yorodumi
- PDB-3ktm: Structure of the Heparin-induced E1-Dimer of the Amyloid Precurso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ktm
TitleStructure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)
ComponentsAmyloid beta A4 protein
KeywordsCELL ADHESION / SIGNALING PROTEIN / Protein Structure / Alzheimer disease / Amyloid / Amyloidosis / Apoptosis / Copper / Disease mutation / Disulfide bond / Endocytosis / Heparin-binding / Metal-binding / Neurodegeneration / Notch signaling pathway / Proteoglycan / Zinc
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / regulation of synapse structure or activity / hippocampal neuron apoptotic process / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / PTB domain binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Golgi-associated vesicle / astrocyte projection / Lysosome Vesicle Biogenesis / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / dendrite development / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / The NLRP3 inflammasome / main axon / regulation of multicellular organism growth / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / response to insulin-like growth factor stimulus / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / cellular response to manganese ion / positive regulation of chemokine production / Notch signaling pathway / swimming behavior / extracellular matrix organization / neuron projection maintenance / clathrin-coated pit / astrocyte activation / axonogenesis / positive regulation of mitotic cell cycle / Mitochondrial protein degradation / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / response to interleukin-1 / regulation of neuron apoptotic process / cellular response to copper ion / cellular response to cAMP / positive regulation of glycolytic process / endosome lumen / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / dendritic shaft / central nervous system development / positive regulation of interleukin-1 beta production / protein serine/threonine kinase binding / learning / adult locomotory behavior / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / locomotory behavior / microglial cell activation / cellular response to nerve growth factor stimulus / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / regulation of long-term neuronal synaptic plasticity / synapse organization / visual learning / recycling endosome / response to lead ion / positive regulation of interleukin-6 production / positive regulation of JNK cascade / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / positive regulation of tumor necrosis factor production / neuron projection development / positive regulation of inflammatory response / calcium ion transport / Platelet degranulation / regulation of translation / heparin binding / regulation of gene expression
Similarity search - Function
Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / Amyloidogenic glycoprotein, copper-binding domain / 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, heparin-binding / Amyloid A4 N-terminal heparin-binding ...Sugar Binding Protein, Amyloid A4 Protein; Chain A / Amyloidogenic glycoprotein, heparin-binding domain / Amyloidogenic glycoprotein, copper-binding domain / 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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / 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 / Dna Ligase; domain 1 / PH-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (3R)-butane-1,3-diol / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein.
Authors: Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E.
History
DepositionNov 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 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_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
G: Amyloid beta A4 protein
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,53425
Polymers174,0978
Non-polymers1,43717
Water5,080282
1
A: Amyloid beta A4 protein
C: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid beta A4 protein
D: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9567
Polymers43,5242
Non-polymers4315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Amyloid beta A4 protein
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Amyloid beta A4 protein
G: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8606
Polymers43,5242
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
B: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
D: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9483
Polymers21,7621
Non-polymers1862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
E: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
F: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
G: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8522
Polymers21,7621
Non-polymers901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
H: Amyloid beta A4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,7621
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.990, 143.990, 351.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Amyloid beta A4 protein / Alzheimer disease amyloid protein / ABPP / APP


Mass: 21762.080 Da / Num. of mol.: 8 / Fragment: UNP residues 18-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P05067
#2: Chemical
ChemComp-BU4 / (3R)-butane-1,3-diol


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 4.02 Å3/Da / Density % sol: 69.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.7→29 Å / Num. obs: 74422 / % possible obs: 99.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 69.152 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.85 Å / % possible obs: 99.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10822

-
Processing

Software
NameClassification
MxCuBEdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWP, 2FJZ

1mwp

2fjz


Resolution: 2.7→29 Å
RfactorNum. reflection% reflection
Rfree0.2499 3735 5 %
Rwork0.2151 --
all-74570 -
obs-74407 99.8 %
Displacement parametersBiso mean: 48.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11065 0 89 282 11436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007975
X-RAY DIFFRACTIONc_angle_deg1.44886

+
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