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- PDB-5how: X-ray crystallographic structure of an Abeta 17-36 beta-hairpin. ... -

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Basic information

Entry
Database: PDB / ID: 5how
TitleX-ray crystallographic structure of an Abeta 17-36 beta-hairpin. LV(PHI)FAEDCGSNKCAII(SAR)L(ORN)V
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid / oligomer / beta-hairpin / Alzheimer's
Function / homology
Function and homology information


amyloid-beta complex / microglia development / negative regulation of presynapse assembly / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway ...amyloid-beta complex / microglia development / negative regulation of presynapse assembly / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of synapse structure or activity / axo-dendritic transport / regulation of Wnt signaling pathway / axon midline choice point recognition / astrocyte activation involved in immune response / smooth endoplasmic reticulum calcium ion homeostasis / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / suckling behavior / COPII-coated ER to Golgi transport vesicle / positive regulation of protein metabolic process / dendrite development / TRAF6 mediated NF-kB activation / modulation of excitatory postsynaptic potential / presynaptic active zone / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / forebrain development / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / ionotropic glutamate receptor signaling pathway / axonogenesis / response to interleukin-1 / cholesterol metabolic process / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / protein serine/threonine kinase binding / platelet alpha granule lumen / positive regulation of glycolytic process / adult locomotory behavior / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / TAK1-dependent IKK and NF-kappa-B activation / learning / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / visual learning / recycling endosome / neuromuscular junction / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / 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 / Platelet degranulation / cell-cell junction
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 / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.295 Å
AuthorsKreutzer, A.G. / Nowick, J.S. / Spencer, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an A beta 17-36 beta-Hairpin.
Authors: Kreutzer, A.G. / Hamza, I.L. / Spencer, R.K. / Nowick, J.S.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water66737
1
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)28,42312
Polymers28,42312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Buried area11330 Å2
ΔGint-79 kcal/mol
Surface area13490 Å2
MethodPISA
2
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)7,1063
Polymers7,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-11 kcal/mol
Surface area4730 Å2
MethodPISA
3
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Buried area3930 Å2
ΔGint-28 kcal/mol
Surface area8540 Å2
MethodPISA
4
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)7,1063
Polymers7,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area4690 Å2
MethodPISA
5
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein

C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
Buried area4690 Å2
ΔGint-37 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.310, 97.310, 97.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

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Components

#1: Protein/peptide
Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 2368.577 Da / Num. of mol.: 6 / Fragment: UNP residues 687-707 / Mutation: F19PHI, V24C, G29C, G33Sar, M35Orn / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.71 Å3/Da / Density % sol: 73.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1 M HEPES Buffer, 31% (v/v) Jeffamine M-600 / PH range: 6.5-7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 15, 2015
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.295→28.09 Å / Num. obs: 12701 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.05629 / Net I/σ(I): 15.73
Reflection shellResolution: 2.295→2.377 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4378 / Mean I/σ(I) obs: 1.41 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimless0.5.17data scaling
PHASER1.10.1_2155phasing
RefinementResolution: 2.295→28.091 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1270 9.86 %Random selection
Rwork0.2335 ---
obs0.2365 12695 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.295→28.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 0 37 973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005954
X-RAY DIFFRACTIONf_angle_d0.9341278
X-RAY DIFFRACTIONf_dihedral_angle_d20.214606
X-RAY DIFFRACTIONf_chiral_restr0.046150
X-RAY DIFFRACTIONf_plane_restr0.004162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.34490.39061440.37941280X-RAY DIFFRACTION99
2.3449-2.39940.42121380.35221285X-RAY DIFFRACTION100
2.3994-2.45940.36531470.3421308X-RAY DIFFRACTION100
2.4594-2.52580.36041460.34471305X-RAY DIFFRACTION100
2.5258-2.60010.40081440.33181314X-RAY DIFFRACTION100
2.6001-2.6840.38581410.33551281X-RAY DIFFRACTION100
2.684-2.77980.33971390.29621312X-RAY DIFFRACTION100
2.7798-2.8910.29931370.28461299X-RAY DIFFRACTION100
2.891-3.02240.34251430.27581315X-RAY DIFFRACTION100
3.0224-3.18160.3261440.24141297X-RAY DIFFRACTION100
3.1816-3.38060.27471440.25811303X-RAY DIFFRACTION100
3.3806-3.64110.23181400.2361294X-RAY DIFFRACTION100
3.6411-4.00660.22781440.21321301X-RAY DIFFRACTION100
4.0066-4.58420.19591410.16751307X-RAY DIFFRACTION100
4.5842-5.76740.19741400.18171318X-RAY DIFFRACTION100
5.7674-28.0930.23521450.20211302X-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)
14.7812.08184.3053.74175.08968.1116-0.5936-0.57230.5292-0.6310.28230.2275-1.0806-0.05970.39710.432-0.06870.04030.7644-0.0410.559522.288420.738763.1979
24.59782.0637-0.77574.0808-4.50895.62270.1614-0.5592-1.539-1.4863-1.06122.7846-0.7273-1.45631.24491.1852-0.2681-0.30051.81760.01631.196510.863211.119255.9003
33.02233.06891.14098.1614.95483.258-0.5022-1.5709-1.4883-0.71250.15380.19480.0961-1.18970.30840.47650.03670.05940.8270.07170.679922.480418.734566.4217
44.27133.49872.50443.681.52818.4540.52740.6671-0.7372-0.4346-0.68080.15360.2439-0.33160.33750.40930.10760.09190.71710.06850.632721.79125.33756.2899
56.2479-7.356-2.62489.33841.15556.5658-0.6786-0.5493.4669-1.1130.0748-3.025-2.66730.14381.31661.14880.2038-0.08980.88850.24561.275922.784541.439252.2239
63.1687-1.9671.78352.33460.24352.37580.61710.5602-0.1104-0.3651-0.92150.1302-0.1003-0.0050.18010.52560.14750.02650.7171-0.01970.608420.150723.944553.2207
73.3734-2.1213-0.53556.5019-3.66433.7561.45790.7702-0.4869-0.5829-1.365-0.37571.3397-1.67020.28250.63350.0673-0.06560.7274-0.06330.411440.206819.262470.093
82.09351.9336-1.84171.7546-1.64971.5772-0.3469-5.45070.7571.76612.9235-0.7032-1.2283-0.86063.26011.32740.64390.68821.70920.07981.262733.210529.562480.5247
92.82242.81283.64767.59788.09189.51760.2031-1.01540.67462.47070.8506-0.36512.44140.0442-1.16040.6238-0.0330.06050.6616-0.10750.540938.308121.117875.5853
104.6327-0.54633.12683.7256-2.22673.0875-1.07370.96790.44571.7195-0.073-1.8392.4001-0.4488-0.7420.7686-0.0754-0.15120.5374-0.07230.537639.17019.756265.6896
114.49120.16340.494.44535.13795.97240.87411.0454-0.41110.7537-1.6562-0.60011.51061.7420.38670.68670.0621-0.16880.5415-0.0290.665746.764411.735966.5719
127.47885.5691-2.52214.6317-2.8954.1571-0.07210.36660.1207-0.03-0.3137-1.12640.40730.65640.33290.551-0.0084-0.05630.61390.03770.526749.259616.687162.3261
139.3543-2.0994-1.1324.6889-1.80217.90510.14-0.19850.3371-0.07310.7684-0.35020.744-0.4856-0.9420.59070.22480.01690.6478-0.08740.542425.785927.666469.2083
144.3669-0.8835-0.41488.1475-4.45793.7292-0.4961-0.01720.0571-0.12030.1142-0.88580.0884-0.35340.16110.58910.02740.02420.5046-0.04440.50427.113931.83763.0438
158.0323-0.5842-7.88287.4467-0.18848.7510.1060.8880.64790.37120.0152-0.252-0.19480.03250.34340.4411-0.1466-0.10420.7897-0.12150.516344.404825.283366.2753
165.48190.2964.90921.27880.65158.2108-3.7931-0.08791.4279-1.55184.101-1.99660.1141-0.3549-0.47711.4879-0.15060.5691.4369-0.56861.894558.531629.186958.8153
172.341.67620.19473.3557-2.96774.344-0.1618-0.04041.5613-0.24-0.13710.5272-0.4746-0.16110.51780.5450.0017-0.03720.446-0.07030.678743.304128.760466.9214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 6 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 21 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 6 )
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 11 )
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 17 )
10X-RAY DIFFRACTION10chain 'C' and (resid 19 through 21 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 21 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 11 )
14X-RAY DIFFRACTION14chain 'E' and (resid 12 through 21 )
15X-RAY DIFFRACTION15chain 'F' and (resid 1 through 6 )
16X-RAY DIFFRACTION16chain 'F' and (resid 7 through 11 )
17X-RAY DIFFRACTION17chain 'F' and (resid 12 through 21 )

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