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- PDB-3q7g: Crystal Structure of E2 domain of Human Amyloid Precursor-Like Pr... -

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Basic information

Entry
Database: PDB / ID: 3q7g
TitleCrystal Structure of E2 domain of Human Amyloid Precursor-Like Protein 1 in complex with SOS (sucrose octasulfate)
ComponentsAmyloid-like protein 1
KeywordsSIGNALING PROTEIN / Amyloid beta precursor protein / E2 domain / Alzheimer's disease / signaling / Heparin
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
sucrose octasulfate / Amyloid beta precursor like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXue, Y. / Ha, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of the E2 Domain of Amyloid Precursor Protein-like Protein 1 in Complex with Sucrose Octasulfate.
Authors: Xue, Y. / Lee, S. / Wang, Y. / Ha, Y.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6245
Polymers49,6762
Non-polymers2,9483
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-42 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.548, 82.236, 89.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24838.010 Da / Num. of mol.: 2 / Fragment: E2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51693
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6.5
Details: 25% PEG 3350, 0.1 M bis-tris, 0.2 M Li2SO4, 25 mM ATP, pH 6.5, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2010 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 24869 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.491 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.39 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.77 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26053 2367 9.8 %RANDOM
Rwork0.2171 ---
obs0.22152 21672 97.04 %-
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 mean: 55.538 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2--0.57 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 165 162 3349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4672.0094465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.0235396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30723.487152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40915506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571532
X-RAY DIFFRACTIONr_chiral_restr0.0890.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212384
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.1631.51988
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.64223146
X-RAY DIFFRACTIONr_scbond_it15.97331270
X-RAY DIFFRACTIONr_scangle_it20.5654.51319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 179 -
Rwork0.264 1464 -
obs--92.25 %
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)
10.4705-0.31510.03941.5501-1.99581.7759-0.1907-0.09620.14020.26690.1047-0.1414-0.1498-0.11190.0860.16750.0503-0.07370.0366-0.01620.062816.3839-22.776938.6486
21.1660.1609-0.56771.0455-1.46581.4667-0.14550.1508-0.09110.01820.111-0.01810.0825-0.08090.03450.0720.02990.0460.1226-0.02310.057235.7911-56.899239.4028
32.5234-0.83471.10730.3693-0.08430.45420.0062-0.00720.1515-0.0297-0.0554-0.1402-0.0119-0.07770.04910.05580.024-0.00790.1280.06070.081836.6572-44.327521.2583
42.7530.5221.76910.92190.510.98210.0718-0.04170.2260.084-0.21420.1710.11240.00480.14240.07670.00570.00490.067-0.02880.09193.2863-21.478919.3743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A292 - 379
2X-RAY DIFFRACTION2A380 - 494
3X-RAY DIFFRACTION3B292 - 379
4X-RAY DIFFRACTION4B380 - 486

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