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- PDB-3pmr: Crystal Structure of E2 domain of Human Amyloid Precursor-Like Pr... -

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Basic information

Entry
Database: PDB / ID: 3pmr
TitleCrystal Structure of E2 domain of Human Amyloid Precursor-Like Protein 1
ComponentsAmyloid-like protein 1
KeywordsCELL ADHESION / 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 / regulation of translation / heparin binding / nervous system development / 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
PHOSPHATE ION / Amyloid beta precursor like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsLee, S. / Xue, Y. / Hu, J. / Wang, Y. / Liu, X. / Demeler, B. / Ha, Y.
CitationJournal: Biochemistry / Year: 2011
Title: The E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization.
Authors: Lee, S. / Xue, Y. / Hu, J. / Wang, Y. / Liu, X. / Demeler, B. / Ha, Y.
History
DepositionNov 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2023Group: Database references / Derived calculations / Category: database_2 / 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0196
Polymers50,6392
Non-polymers3804
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-41 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.885, 81.269, 89.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25319.555 Da / Num. of mol.: 2 / Fragment: E2 domain (UNP residues 285-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51693
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.4M Na/K Phosphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 32194 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.402 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→39.26 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.326 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 3033 10 %RANDOM
Rwork0.2078 ---
obs0.2113 30452 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 142.92 Å2 / Biso mean: 43.7544 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--1.57 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.11→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 20 277 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213109
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9524206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.9135391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.423.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27515531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6771535
X-RAY DIFFRACTIONr_chiral_restr0.0790.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212373
X-RAY DIFFRACTIONr_mcbond_it5.7521.51963
X-RAY DIFFRACTIONr_mcangle_it7.8323120
X-RAY DIFFRACTIONr_scbond_it11.93131146
X-RAY DIFFRACTIONr_scangle_it16.5384.51086
LS refinement shellResolution: 2.108→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 208 -
Rwork0.239 1846 -
all-2054 -
obs--91.82 %
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)
10.288-0.017-0.07940.6075-0.68450.72-0.0782-0.08230.03730.08970.0571-0.0153-0.0778-0.04950.02110.13720.0473-0.01870.0828-0.01280.057416.9112-22.50938.1738
20.163-0.0123-0.24820.6193-0.45150.8221-0.11820.0637-0.07880.059-0.041-0.060.0214-0.09280.15920.11110.01320.06140.09840.01770.096636.9145-57.136840.3639
31.4042-0.63010.60170.5296-0.03870.37920.03510.00130.0334-0.0193-0.0456-0.05980.0124-0.05730.01050.06960.03670.01180.1220.0360.065237.2252-44.252521.1981
41.8442-0.07820.93480.65010.02080.75190.0281-0.02960.0880.1007-0.08690.16930.06870.00540.05870.0584-0.00140.0130.0555-0.02240.1183.6543-21.162219.9589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A354 - 441
2X-RAY DIFFRACTION2A442 - 548
3X-RAY DIFFRACTION3B354 - 441
4X-RAY DIFFRACTION4B442 - 551

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