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- PDB-9zip: Crystal Structure of RASProtease(II), a Designed RAS-specific Sub... -

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Basic information

Entry
Database: PDB / ID: 9zip
TitleCrystal Structure of RASProtease(II), a Designed RAS-specific Subtilisin, in Complex with the Cognate Peptide QEEYSAM
Components
  • Peptide QEEYSAM
  • SUBTILISIN BPN'
KeywordsHYDROLASE / Engineered protease
Function / homologyACETATE ION / :
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsChu, B. / Toth, E.A. / Orban, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biorxiv / Year: 2026
Title: Substrate specificity in a designed RAS-targeting protease is coupled to active site and distal motions.
Authors: Chu, B. / He, Y. / Chen, Y. / Toth, E.A. / Orban, J.
History
DepositionDec 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: SUBTILISIN BPN'
A: SUBTILISIN BPN'
B: Peptide QEEYSAM
C: Peptide QEEYSAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92321
Polymers54,8234
Non-polymers1,10017
Water9,368520
1
S: SUBTILISIN BPN'
B: Peptide QEEYSAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,98111
Polymers27,4122
Non-polymers5709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-1 kcal/mol
Surface area9890 Å2
MethodPISA
2
A: SUBTILISIN BPN'
C: Peptide QEEYSAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,94210
Polymers27,4122
Non-polymers5318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-1 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.978, 57.909, 82.488
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules SABC

#1: Protein SUBTILISIN BPN'


Mass: 26554.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Peptide QEEYSAM


Mass: 856.897 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 537 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 50 mM zinc acetate, 10 mM imidazole, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→47.24 Å / Num. obs: 107996 / % possible obs: 94 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Χ2: 1.1 / Net I/σ(I): 18 / Num. measured all: 646759
Reflection shellResolution: 1.24→1.26 Å / % possible obs: 86.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.297 / Num. measured all: 28696 / Num. unique obs: 4939 / CC1/2: 0.965 / Rpim(I) all: 0.133 / Rrim(I) all: 0.326 / Χ2: 0.41 / Net I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→47.24 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 13.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1397 5351 4.99 %
Rwork0.1127 --
obs0.1141 107129 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 67 520 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134255
X-RAY DIFFRACTIONf_angle_d1.6225851
X-RAY DIFFRACTIONf_dihedral_angle_d8.641678
X-RAY DIFFRACTIONf_chiral_restr0.117690
X-RAY DIFFRACTIONf_plane_restr0.014766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.17621560.14223073X-RAY DIFFRACTION83
1.26-1.270.16311530.12623275X-RAY DIFFRACTION91
1.27-1.290.18321860.12063339X-RAY DIFFRACTION92
1.29-1.30.14851790.10913331X-RAY DIFFRACTION93
1.3-1.320.15391670.10193374X-RAY DIFFRACTION93
1.32-1.340.1372040.09683336X-RAY DIFFRACTION93
1.34-1.360.15151750.09443350X-RAY DIFFRACTION93
1.36-1.380.15321660.0933465X-RAY DIFFRACTION94
1.38-1.40.13721740.09593432X-RAY DIFFRACTION94
1.4-1.420.12521770.09763414X-RAY DIFFRACTION93
1.42-1.450.15091740.10163358X-RAY DIFFRACTION94
1.45-1.470.14071480.1033306X-RAY DIFFRACTION90
1.47-1.50.14061760.09913140X-RAY DIFFRACTION87
1.5-1.530.13631820.09873472X-RAY DIFFRACTION95
1.53-1.570.13721940.08833450X-RAY DIFFRACTION95
1.57-1.60.13041760.09043457X-RAY DIFFRACTION96
1.6-1.640.12251580.09043510X-RAY DIFFRACTION95
1.64-1.690.13761950.09213512X-RAY DIFFRACTION96
1.69-1.740.12011670.09143506X-RAY DIFFRACTION96
1.74-1.790.13741730.10093501X-RAY DIFFRACTION96
1.79-1.860.11751800.10143516X-RAY DIFFRACTION96
1.86-1.930.11721980.10153448X-RAY DIFFRACTION95
1.93-2.020.12611820.10443126X-RAY DIFFRACTION86
2.02-2.130.11341700.10133361X-RAY DIFFRACTION92
2.13-2.260.11241820.10693534X-RAY DIFFRACTION96
2.26-2.430.13521920.11673552X-RAY DIFFRACTION97
2.43-2.680.15712070.12163471X-RAY DIFFRACTION96
2.68-3.070.14671910.13243492X-RAY DIFFRACTION95
3.07-3.860.15251740.12863074X-RAY DIFFRACTION83

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