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- PDB-5tpt: The Crystal Structure of Amyloid Precursor-Like Protein 2 (APLP2)... -

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Basic information

Entry
Database: PDB / ID: 5tpt
TitleThe Crystal Structure of Amyloid Precursor-Like Protein 2 (APLP2) E2 Domain
ComponentsAmyloid-like protein 2
KeywordsPROTEIN FIBRIL / Amyloid Precursor Protein family / Alzheimer's disease
Function / homology
Function and homology information


negative regulation of peptidase activity / platelet alpha granule membrane / transition metal ion binding / axonogenesis / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / heparin binding ...negative regulation of peptidase activity / platelet alpha granule membrane / transition metal ion binding / axonogenesis / central nervous system development / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / heparin binding / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / DNA binding / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Amyloid precursor protein, E2 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. / 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, E2 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. / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Amyloid beta precursor like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.422 Å
AuthorsRoisman, L.C. / Cappai, R.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian National Health and Medical Research Council566575; 509040; 628946 Australia
Australian Research CouncilDP1096225 Australia
CitationJournal: Faseb J. / Year: 2019
Title: The crystal structure of amyloid precursor-like protein 2 E2 domain completes the amyloid precursor protein family.
Authors: Roisman, L.C. / Han, S. / Chuei, M.J. / Connor, A.R. / Cappai, R.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _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 / _pdbx_contact_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid-like protein 2
B: Amyloid-like protein 2


Theoretical massNumber of molelcules
Total (without water)47,0632
Polymers47,0632
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-8 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.749, 150.118, 39.107
Angle α, β, γ (deg.)90.000, 109.690, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPARGARGchain AAA373 - 5691 - 197
2HISHISGLUGLUchain BBB387 - 56715 - 195

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Components

#1: Protein Amyloid-like protein 2 / APLP-2 / APPH / Amyloid protein homolog / CDEI box-binding protein / CDEBP


Mass: 23531.742 Da / Num. of mol.: 2 / Fragment: UNP residues 373-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP2, APPL2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06481
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: 0.1 M phosphate-citrate, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.42→37.53 Å / Num. obs: 14709 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.59 Å2 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.058 / Rrim(I) all: 0.148 / Net I/σ(I): 9.3 / Num. measured all: 94037
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.42-2.516.40.841199.3
8.83-37.536.10.03199.3

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Processing

Software
NameVersionClassification
Aimless0.1.2data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3umi

3umi


Resolution: 2.422→37.529 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.13
RfactorNum. reflection% reflection
Rfree0.2595 1468 10 %
Rwork0.2137 --
obs0.2184 14677 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.76 Å2 / Biso mean: 44.7406 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 2.422→37.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 0 75 3244
Biso mean---37.51 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043219
X-RAY DIFFRACTIONf_angle_d0.7174326
X-RAY DIFFRACTIONf_chiral_restr0.03467
X-RAY DIFFRACTIONf_plane_restr0.004575
X-RAY DIFFRACTIONf_dihedral_angle_d14.3551291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1766X-RAY DIFFRACTION3.787TORSIONAL
12B1766X-RAY DIFFRACTION3.787TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.422-2.50850.27811440.24131292143699
2.5085-2.60890.28491470.24521325147299
2.6089-2.72770.29561460.24991322146899
2.7277-2.87140.30831450.23741308145399
2.8714-3.05120.28811480.221513201468100
3.0512-3.28670.28091480.233413361484100
3.2867-3.61720.29041470.201113191466100
3.6172-4.14010.22121440.19412971441100
4.1401-5.21380.21471490.187813441493100
5.2138-37.5340.24941500.213713461496100

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