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- PDB-4e1h: Fragment of human prion protein -

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Basic information

Entry
Database: PDB / ID: 4e1h
TitleFragment of human prion protein
Components(Major prion protein) x 2
KeywordsCELL CYCLE / beta prism / amyloid-related oligomer / PROTEIN FIBRIL
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / negative regulation of DNA-binding transcription factor activity / protein homooligomerization / terminal bouton / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / postsynapse / transmembrane transporter binding / response to oxidative stress / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
CITRIC ACID / : / Major prion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsApostol, M.I. / Perry, K. / Surewicz, W.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Crystal structure of a human prion protein fragment reveals a motif for oligomer formation.
Authors: Apostol, M.I. / Perry, K. / Surewicz, W.K.
History
DepositionMar 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 16, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
B: Major prion protein
C: Major prion protein
D: Major prion protein
E: Major prion protein
F: Major prion protein
G: Major prion protein
H: Major prion protein
I: Major prion protein
J: Major prion protein
K: Major prion protein
L: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,48419
Polymers8,54812
Non-polymers9367
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-89 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.317, 42.898, 46.353
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/peptide
Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 700.784 Da / Num. of mol.: 6 / Fragment: UNP residues 177-182 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#2: Protein/peptide
Major prion protein / PrP / ASCR / PrP27-30 / PrP33-35C


Mass: 723.858 Da / Num. of mol.: 6 / Fragment: UNP residues 211-216 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04156
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.88 Å3/Da / Density % sol: 34.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100mM Citrate pH 3.5, 10mM iron (II) chloride, and 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.73964
SYNCHROTRONAPS 24-ID-C20.97918
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 27, 2010
ADSC QUANTUM 3152CCDNov 27, 2010
Radiation
IDProtocolScattering typeWavelength-ID
1SADx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.739641
20.979181
ReflectionRedundancy: 14.5 % / Av σ(I) over netI: 29.15 / Number: 129810 / Rmerge(I) obs: 0.083 / Χ2: 1.78 / D res high: 1.96 Å / D res low: 30 Å / Num. obs: 8953 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.223099.710.0492.79815
3.354.2210010.0682.52514.6
2.933.3510010.0912.34114.8
2.662.9310010.0962.01914.7
2.472.6610010.1161.76814.6
2.322.4710010.1441.56414.5
2.212.3210010.1961.40814.4
2.112.2110010.2381.23714.4
2.032.1110010.3331.00714.2
1.962.0397.410.4210.96813.7
ReflectionResolution: 1.4→30 Å / Num. obs: 13272 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.059 / Χ2: 1.217 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.454.60.75613070.5691,2100
1.45-1.514.70.54212870.6181,2100
1.51-1.584.70.38312990.671,2100
1.58-1.664.60.28913200.7871,2100
1.66-1.764.60.20513000.9531,2100
1.76-1.94.60.14313171.3561,2100
1.9-2.094.60.10513321.8081,299.8
2.09-2.394.60.08313152.0171,299.9
2.39-3.024.50.05313671.7931,299.9
3.02-304.40.03314281.5831,298.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Adxvdata processing
SHELXDphasing
RefinementResolution: 1.4→22.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.167 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 649 4.9 %RANDOM
Rwork0.164 ---
obs0.167 12531 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms576 0 55 56 687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021722
X-RAY DIFFRACTIONr_bond_other_d0.0050.02402
X-RAY DIFFRACTIONr_angle_refined_deg1.7512.033992
X-RAY DIFFRACTIONr_angle_other_deg1.88731034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.611578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45127.89538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14715134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02770
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0286
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_it2.7931.5406
X-RAY DIFFRACTIONr_mcbond_other0.8751.5146
X-RAY DIFFRACTIONr_mcangle_it4.3992676
X-RAY DIFFRACTIONr_scbond_it5.9523316
X-RAY DIFFRACTIONr_scangle_it8.3894.5302
X-RAY DIFFRACTIONr_rigid_bond_restr2.73831124
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 59 -
Rwork0.235 889 -
obs--98.96 %
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)
10.6296-0.0081-0.37681.3790.68630.890.01680.00160.01240.0553-0.00940.02070.0579-0.0274-0.00740.0102-0.0014-0.0050.00540.00190.01714.180919.631614.3858
20.4594-0.44240.17233.06141.99762.11820.039-0.0059-0.0209-0.0141-0.01180.06980.0484-0.0516-0.02720.0057-0.0027-0.00120.00550.00480.02354.809218.598223.2379
30.75970.1507-0.47420.58720.07890.4132-0.0175-0.0003-0.0033-0.00960.0159-0.04230.01210.00050.00150.0061-0.00020.0010.0074-0.00070.020617.739127.455323.264
40.4392-0.6656-0.14852.31720.49750.35350.01690.0124-0.0096-0.0343-0.01520.00950.00420.0044-0.00180.0056-0.0005-0.00180.00780.00070.019216.817228.436313.6636
50.215-0.21550.02110.47640.29170.3416-0.0109-0.00740.02010.00530.0152-0.00960.00440.011-0.00430.00930-0.00280.0075-0.00120.02747.904229.143912.9383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A177 - 182
2X-RAY DIFFRACTION2C177 - 182
3X-RAY DIFFRACTION3E177 - 182
4X-RAY DIFFRACTION4I177 - 182
5X-RAY DIFFRACTION5K177 - 182

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