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- PDB-9ccf: Crystal Structure of DA7-2 -

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Basic information

Entry
Database: PDB / ID: 9ccf
TitleCrystal Structure of DA7-2
ComponentsDA7_2
KeywordsDE NOVO PROTEIN / de novo design / disorder / intrinsically disordered protein
Function / homology
Function and homology information


opioid peptide activity / Opioid Signalling / sensory perception / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / G-protein activation / G alpha (i) signalling events ...opioid peptide activity / Opioid Signalling / sensory perception / neuropeptide signaling pathway / neuronal dense core vesicle / axon terminus / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / G-protein activation / G alpha (i) signalling events / chemical synaptic transmission / neuronal cell body / dendrite / extracellular region / plasma membrane
Similarity search - Function
Proenkephalin B / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBera, A.K. / Wu, K. / Kang, A. / Baker, D.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Science / Year: 2025
Title: Design of intrinsically disordered region binding proteins.
Authors: Wu, K. / Jiang, H. / Hicks, D.R. / Liu, C. / Muratspahic, E. / Ramelot, T.A. / Liu, Y. / McNally, K. / Kenny, S. / Mihut, A. / Gaur, A. / Coventry, B. / Chen, W. / Bera, A.K. / Kang, A. / ...Authors: Wu, K. / Jiang, H. / Hicks, D.R. / Liu, C. / Muratspahic, E. / Ramelot, T.A. / Liu, Y. / McNally, K. / Kenny, S. / Mihut, A. / Gaur, A. / Coventry, B. / Chen, W. / Bera, A.K. / Kang, A. / Gerben, S. / Lamb, M.Y. / Murray, A. / Li, X. / Kennedy, M.A. / Yang, W. / Song, Z. / Schober, G. / Brierley, S.M. / O'Neill, J. / Gelb, M.H. / Montelione, G.T. / Derivery, E. / Baker, D.
History
DepositionJun 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DA7_2
B: DA7_2


Theoretical massNumber of molelcules
Total (without water)56,3582
Polymers56,3582
Non-polymers00
Water00
1
A: DA7_2


Theoretical massNumber of molelcules
Total (without water)28,1791
Polymers28,1791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DA7_2


Theoretical massNumber of molelcules
Total (without water)28,1791
Polymers28,1791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.423, 67.214, 68.361
Angle α, β, γ (deg.)90.000, 96.746, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DA7_2


Mass: 28178.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 2-18 are from Dynorphin A(1-17)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: PDYN / Production host: Escherichia coli (E. coli) / References: UniProt: P01213
Has protein modificationN
Sequence detailsResidues 2-18 are from Dynorphin A(1-17). The remainder is a designed construct.

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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: 1.8 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate pH 4.6 and 25% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 4→47.76 Å / Num. obs: 3361 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 129.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.047 / Net I/σ(I): 11.5
Reflection shellResolution: 4→4.47 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 941 / CC1/2: 0.979 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→47.76 Å / SU ML: 0.3971 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.7706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2963 334 9.99 %
Rwork0.2362 3009 -
obs0.2423 3343 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.1 Å2
Refinement stepCycle: LAST / Resolution: 4→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 0 0 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023237
X-RAY DIFFRACTIONf_angle_d0.4294317
X-RAY DIFFRACTIONf_chiral_restr0.0326497
X-RAY DIFFRACTIONf_plane_restr0.0042557
X-RAY DIFFRACTIONf_dihedral_angle_d14.4191341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-5.040.34081640.25261483X-RAY DIFFRACTION99.34
5.04-47.760.27081700.22681526X-RAY DIFFRACTION98.78

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