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- PDB-4rd9: X-RAY STRUCTURE OF THE APO FORM OF THE AMYLOID PRECURSOR PROTEIN-... -

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Basic information

Entry
Database: PDB / ID: 4rd9
TitleX-RAY STRUCTURE OF THE APO FORM OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 (APLP1) E2 DOMAIN
ComponentsAmyloid-like protein 1
KeywordsSUGAR BINDING PROTEIN / heparin binding
Function / homology
Function and homology information


alpha-2B adrenergic receptor binding / cellular response to norepinephrine stimulus / alpha-2C adrenergic receptor binding / alpha-2A adrenergic receptor binding / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytosolic mRNA polyadenylation / basement membrane / transition metal ion binding / forebrain development / extracellular matrix organization ...alpha-2B adrenergic receptor binding / cellular response to norepinephrine stimulus / alpha-2C adrenergic receptor binding / alpha-2A adrenergic receptor binding / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytosolic mRNA polyadenylation / basement membrane / transition metal ion binding / forebrain development / extracellular matrix organization / axonogenesis / central nervous system development / animal organ morphogenesis / endocytosis / nervous system development / regulation of translation / heparin binding / cell adhesion / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / identical protein binding / 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. / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Amyloid beta precursor like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsDahms, S.O. / Than, M.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes.
Authors: Dahms, S.O. / Mayer, M.C. / Roeser, D. / Multhaup, G. / Than, M.E.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid-like protein 1
B: Amyloid-like protein 1


Theoretical massNumber of molelcules
Total (without water)47,3452
Polymers47,3452
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.425, 79.145, 95.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsx, y, z

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Components

#1: Protein Amyloid-like protein 1 / APLP / APLP-1 / C30


Mass: 23672.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP1 / Production host: Pichia pastoris (fungus) / References: UniProt: P51693
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Na-Citrate, 0.9 M(NH4)H2PO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 8, 2013 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→34.76 Å / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2299 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.6→33.997 Å / SU ML: 0.36 / σ(F): 1.25 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1544 5.18 %
Rwork0.2153 --
obs0.2169 29832 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→33.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 0 47 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033179
X-RAY DIFFRACTIONf_angle_d0.6374287
X-RAY DIFFRACTIONf_dihedral_angle_d17.8971257
X-RAY DIFFRACTIONf_chiral_restr0.024461
X-RAY DIFFRACTIONf_plane_restr0.004587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.40411020.28762607X-RAY DIFFRACTION100
2.6839-2.77980.31592070.26062531X-RAY DIFFRACTION100
2.7798-2.89110.2671050.24812613X-RAY DIFFRACTION100
2.8911-3.02260.27891040.25352615X-RAY DIFFRACTION100
3.0226-3.18180.30122070.25612500X-RAY DIFFRACTION100
3.1818-3.3810.24311030.22782569X-RAY DIFFRACTION100
3.381-3.64170.23571070.20122607X-RAY DIFFRACTION100
3.6417-4.00770.2282100.19162534X-RAY DIFFRACTION100
4.0077-4.58640.29211040.18432577X-RAY DIFFRACTION100
4.5864-5.77380.21182020.20112517X-RAY DIFFRACTION100
5.7738-33.99950.1853930.20872618X-RAY DIFFRACTION100
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)
1-0.1754-0.12320.18430.31510.19590.283-0.0616-0.0197-0.0012-0.09160.00490.00150.01390.0366-0.00010.3071-0.04110.0290.3481-0.02330.3027-25.1876-2.0119-39.6345
20.47930.26830.36540.38550.07060.1522-0.02490.01830.08870.0218-0.07130.0310.03740.0136-0.00110.2938-0.0357-0.00390.3157-0.04130.3116-14.03079.3144-21.8242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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