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- PDB-9nzh: Crystal Structure of Amylin-NHO-18 binder complex -

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Basic information

Entry
Database: PDB / ID: 9nzh
TitleCrystal Structure of Amylin-NHO-18 binder complex
Components
  • Amylin-NHO-18 Binder
  • Islet amyloid polypeptide
KeywordsDE NOVO PROTEIN / protein design / diffusion / deep learning / binders / IDP / IDR / Amyloid / phase separation
Function / homology
Function and homology information


amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells ...amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / Regulation of gene expression in beta cells / positive regulation of cAMP/PKA signal transduction / bone resorption / negative regulation of protein-containing complex assembly / sensory perception of pain / positive regulation of calcium-mediated signaling / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / positive regulation of apoptotic process / receptor ligand activity / Amyloid fiber formation / signaling receptor binding / neuronal cell body / apoptotic process / lipid binding / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
Islet amyloid polypeptide
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBera, A.K. / Lui, C. / Kang, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Diffusing protein binders to intrinsically disordered proteins
Authors: Liu, C. / Bera, A.K. / Baker, D.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amylin-NHO-18 Binder
B: Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8494
Polymers19,6572
Non-polymers1922
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-46 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.189, 59.189, 90.946
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-353-

HOH

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Components

#1: Protein Amylin-NHO-18 Binder


Mass: 15748.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Islet amyloid polypeptide / Amylin / Diabetes-associated peptide / DAP / Insulinoma amyloid peptide


Mass: 3909.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10997
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 3.2 M Ammonium sulfate, 0.1 M Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92017 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2025 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92017 Å / Relative weight: 1
ReflectionResolution: 2.03→34.02 Å / Num. obs: 12402 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.109 / Net I/σ(I): 5.1
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1771 / CC1/2: 0.428 / Rpim(I) all: 0.613 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→34.02 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.0608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 1241 10.03 %
Rwork0.1842 11135 -
obs0.1895 12376 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 2.03→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 10 78 1421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481358
X-RAY DIFFRACTIONf_angle_d0.66441827
X-RAY DIFFRACTIONf_chiral_restr0.046216
X-RAY DIFFRACTIONf_plane_restr0.0034233
X-RAY DIFFRACTIONf_dihedral_angle_d20.6049525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.110.32971380.25941215X-RAY DIFFRACTION100
2.11-2.210.29631330.2331215X-RAY DIFFRACTION100
2.21-2.320.291360.21481214X-RAY DIFFRACTION100
2.32-2.470.26311350.22071217X-RAY DIFFRACTION100
2.47-2.660.24961340.20281215X-RAY DIFFRACTION99.93
2.66-2.930.23721390.18951235X-RAY DIFFRACTION99.93
2.93-3.350.2561390.1791234X-RAY DIFFRACTION100
3.35-4.220.1961340.13951265X-RAY DIFFRACTION100
4.22-34.020.18921530.16761325X-RAY DIFFRACTION100

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