[English] 日本語
Yorodumi
- PDB-2ipu: PFA1 Fab fragment complexed with Abeta 1-8 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ipu
TitlePFA1 Fab fragment complexed with Abeta 1-8 peptide
Components
  • (IgG2a Fab fragment ...) x 2
  • abeta 1-8 peptide
KeywordsIMMUNE SYSTEM / wwddd / cdr / abeta
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
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. / 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 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 / : / 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. / PH-like domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETAMIDE / If kappa light chain / Amyloid-beta precursor protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGardberg, A.S. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis for passive immunotherapy of Alzheimer's disease
Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _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
Remark 999SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: IgG2a Fab fragment Heavy Chain
H: IgG2a Fab fragment Light Chain Kappa
K: IgG2a Fab fragment Heavy Chain
G: IgG2a Fab fragment Light Chain Kappa
P: abeta 1-8 peptide
Q: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,17015
Polymers98,4406
Non-polymers7309
Water2,126118
1
L: IgG2a Fab fragment Heavy Chain
H: IgG2a Fab fragment Light Chain Kappa
Q: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6148
Polymers49,2203
Non-polymers3945
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: IgG2a Fab fragment Heavy Chain
G: IgG2a Fab fragment Light Chain Kappa
P: abeta 1-8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5557
Polymers49,2203
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.070, 70.335, 74.197
Angle α, β, γ (deg.)72.32, 86.08, 86.02
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a heterodimer with abeta peptide at the interface.

-
Components

-
Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide abeta 1-8 peptide


Mass: 977.975 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (humans)
References: UniProt: P05067*PLUS

-
Antibody , 2 types, 4 molecules LKHG

#1: Antibody IgG2a Fab fragment Heavy Chain


Mass: 24146.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3*PLUS
#2: Antibody IgG2a Fab fragment Light Chain Kappa


Mass: 24095.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c

-
Non-polymers , 3 types, 127 molecules

#4: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, temperature 294K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.65→23.53 Å / Num. obs: 90408 / % possible obs: 90.7 % / Redundancy: 3.1 % / Rsym value: 0.055
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.467 / % possible all: 66.3

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IQ9

2iq9


Resolution: 1.65→23.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.106 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4515 5 %RANDOM
Rwork0.182 ---
obs0.184 90407 90.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.01 Å20.2 Å2
2---0.01 Å2-0.59 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→23.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 48 118 7012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227230
X-RAY DIFFRACTIONr_bond_other_d0.0010.024840
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9559898
X-RAY DIFFRACTIONr_angle_other_deg0.876311887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3323.818275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.138151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751533
X-RAY DIFFRACTIONr_chiral_restr0.0870.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021445
X-RAY DIFFRACTIONr_nbd_refined0.1880.21106
X-RAY DIFFRACTIONr_nbd_other0.20.24918
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23353
X-RAY DIFFRACTIONr_nbtor_other0.0850.23916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2533
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.274
X-RAY DIFFRACTIONr_mcbond_it1.0451.55871
X-RAY DIFFRACTIONr_mcbond_other0.1921.51835
X-RAY DIFFRACTIONr_mcangle_it1.23427438
X-RAY DIFFRACTIONr_scbond_it1.95433178
X-RAY DIFFRACTIONr_scangle_it2.6134.52426
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 206 -
Rwork0.325 4083 -
obs-4289 58.59 %

+
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