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- PDB-9zye: Crystal structure of HTLV-1 protease bound to UMass6 at 2.7 angst... -

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Basic information

Entry
Database: PDB / ID: 9zye
TitleCrystal structure of HTLV-1 protease bound to UMass6 at 2.7 angstroms with truncated flaps
ComponentsHTLV-1 Protease
KeywordsVIRAL PROTEIN/INHIBITOR / HTLV-1 / PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-A60 / Pro protein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShaqra, A.M. / Lockbaum, G.J. / Intravaia, L.E. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: Crystal structure of HTLV-1 protease bound to UMass6 at 2.7 angstroms with truncated flaps
Authors: Shaqra, A.M. / Lockbaum, G.J. / Intravaia, L.E. / Schiffer, C.A.
History
DepositionJan 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HTLV-1 Protease
A: HTLV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9034
Polymers25,1332
Non-polymers7702
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-18 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.753, 77.753, 159.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-348-

HOH

21A-319-

HOH

31A-334-

HOH

41A-343-

HOH

51A-344-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 9 or resid 11...
d_2ens_1(chain "B" and (resid 1 through 9 or resid 11...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROARGARGAB1 - 91 - 9
d_12PROPROTHRTHRAB11 - 2111 - 21
d_13PROPROASNASNAB24 - 5324 - 53
d_14HISHISTHRTHRAB66 - 8866 - 88
d_15LEULEUVALVALAB91 - 11291 - 112
d_16TYRTYRPROPROAB114 - 116114 - 116
d_21PROPROARGARGBA1 - 91 - 9
d_22PROPROTHRTHRBA11 - 2111 - 21
d_23PROPROTHRTHRBA24 - 8824 - 88
d_24LEULEUVALVALBA91 - 11291 - 112
d_25TYRTYRPROPROBA114 - 116114 - 116

NCS oper: (Code: givenMatrix: (-0.998663544204, -0.0228505537383, 0.0463570671117), (0.0116018995392, -0.973176949869, -0.229765141329), (0.0503638898858, -0.228920240339, 0.972141451723)Vector: -78. ...NCS oper: (Code: given
Matrix: (-0.998663544204, -0.0228505537383, 0.0463570671117), (0.0116018995392, -0.973176949869, -0.229765141329), (0.0503638898858, -0.228920240339, 0.972141451723)
Vector: -78.501004658, 4.98406259866, 2.54951380182)

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Components

#1: Protein HTLV-1 Protease


Mass: 12566.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pro / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1C9N2
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-A60 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate


Mass: 575.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N3O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.7→41.67 Å / Num. obs: 8385 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 58.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.012 / Rpim(I) all: 0.012 / Rrim(I) all: 0.017 / Net I/σ(I): 32.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 806 / CC1/2: 0.978 / Rpim(I) all: 0.093 / Rrim(I) all: 0.132

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.67 Å / SU ML: 0.225 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.5387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.282 420 5.01 %
Rwork0.2225 7959 -
obs0.2254 8379 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 53 92 1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861697
X-RAY DIFFRACTIONf_angle_d0.9592344
X-RAY DIFFRACTIONf_chiral_restr0.0558301
X-RAY DIFFRACTIONf_plane_restr0.0076290
X-RAY DIFFRACTIONf_dihedral_angle_d13.5873247
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.750585080501 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.090.37571350.32852560X-RAY DIFFRACTION99.96
3.09-3.890.26461370.21792611X-RAY DIFFRACTION99.85
3.89-41.670.26691480.19952788X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -38.8705382314 Å / Origin y: -0.114572108106 Å / Origin z: 19.3407899663 Å
111213212223313233
T0.349135677623 Å20.0304371955965 Å20.0327535088928 Å2-0.267032558452 Å2-0.0312644886692 Å2--0.307924419675 Å2
L8.22094824902 °21.73564348869 °20.334144184608 °2-2.73712549571 °20.0385063390066 °2--0.438475906638 °2
S0.133513633321 Å °0.0159669646702 Å °0.000385683672735 Å °0.0642862690115 Å °-0.185454093762 Å °0.0735333530792 Å °0.0354884826012 Å °-0.0186802347399 Å °0.0489908368603 Å °
Refinement TLS groupSelection details: all

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