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- PDB-2b7f: Crystal structure of human T-cell leukemia virus protease, a nove... -

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Basic information

Entry
Database: PDB / ID: 2b7f
TitleCrystal structure of human T-cell leukemia virus protease, a novel target for anti-cancer design
Components
  • (ACE)APQV(STA)VMHP peptide
  • HTLV protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host translation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity ...symbiont-mediated suppression of host translation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / nucleic acid binding / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / structural molecule activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
: / Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral ...: / Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Integrase Zinc binding domain / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(ACE)APQV(STA)VMHP peptide Inhibitor / PHOSPHATE ION / Gag-Pro-Pol polyprotein / Gag-Pro polyprotein
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, M. / Laco, G.S. / Jaskolski, M. / Rozycki, J. / Alexandratos, J. / Wlodawer, A. / Gustchina, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design
Authors: Li, M. / Laco, G.S. / Jaskolski, M. / Rozycki, J. / Alexandratos, J. / Wlodawer, A. / Gustchina, A.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_id / _struct_conn.ptnr1_label_seq_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 7NCS RESTRAINTS STATISTICS FOR CONFORMATION B OF CHAIN J NCS RESTRAINTS STATISTICS NCS GROUP NUMBER : ...NCS RESTRAINTS STATISTICS FOR CONFORMATION B OF CHAIN J NCS RESTRAINTS STATISTICS NCS GROUP NUMBER : 3 CHAIN NAMES : I J K NUMBER OF COMPONENTS NCS GROUP : 1 COMPONENT C SSSEQI TO C SSSEQI CODE 1 I 401 I 410 1 1 J 401 J 410 1 1 K 401 K 410 1 GROUP CHAIN COUNT RMS WEIGHT TIGHT POSITIONAL 3 I (A): 67 ; 0.08 ; 0.05 TIGHT POSITIONAL 3 J (A): 67 ; 0.06 ; 0.05 TIGHT POSITIONAL 3 K (A): 67 ; 0.06 ; 0.05 TIGHT THERMAL 3 I (A**2): 67 ; 0.21 ; 0.50 TIGHT THERMAL 3 J (A**2): 67 ; 0.17 ; 0.50 TIGHT THERMAL 3 K (A**2): 67 ; 0.18 ; 0.50

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTLV protease
B: HTLV protease
I: (ACE)APQV(STA)VMHP peptide
C: HTLV protease
D: HTLV protease
J: (ACE)APQV(STA)VMHP peptide
E: HTLV protease
F: HTLV protease
K: (ACE)APQV(STA)VMHP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,77611
Polymers78,5869
Non-polymers1902
Water3,099172
1
A: HTLV protease
B: HTLV protease
I: (ACE)APQV(STA)VMHP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers26,1953
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-39 kcal/mol
Surface area11300 Å2
MethodPISA
2
C: HTLV protease
D: HTLV protease
J: (ACE)APQV(STA)VMHP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers26,1953
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-35 kcal/mol
Surface area11310 Å2
MethodPISA
3
E: HTLV protease
F: HTLV protease
K: (ACE)APQV(STA)VMHP peptide


Theoretical massNumber of molelcules
Total (without water)26,1953
Polymers26,1953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-37 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.319, 77.793, 80.376
Angle α, β, γ (deg.)90.00, 99.28, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F
13I
23J
33K

NCS domain segments:

Component-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPRO4AA1 - 1161 - 116
21PROPRO4CD1 - 1161 - 116
31PROPRO4EG1 - 1161 - 116
12PROPRO4BB1 - 1161 - 116
22PROPRO4DE1 - 1161 - 116
32PROPRO4FH1 - 1161 - 116
13ACEACE1IC401 - 4101 - 10
23PROPRO1JF403 - 4103 - 10
33ACEACE1KI401 - 4101 - 10

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
HTLV protease


Mass: 12566.579 Da / Num. of mol.: 6 / Fragment: HTLV Protease Delta-9 (residues 33-148) / Mutation: L40I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / Plasmid: pET-21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P10274, UniProt: P03362*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Protein/peptide (ACE)APQV(STA)VMHP peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1062.303 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: (ACE)APQV(STA)VMHP peptide Inhibitor
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDE INHIBITOR WAS SYNTHESIZED ON AN ABI 431 PEPTIDE SYNTHESIZER (0.25 MM SCALE) STARTING ...THE PEPTIDE INHIBITOR WAS SYNTHESIZED ON AN ABI 431 PEPTIDE SYNTHESIZER (0.25 MM SCALE) STARTING WITH H-PRO-2-CHLOROTRITYL RESIN. STANDARD FASTMOC PROTOCOL WAS USED FOR ALL SYNTHETIC CYCLES EXCEPT FOR THE FMOC-STATINE COUPLING REACTION, WHICH WAS CARRIED OUT MANUALLY FOR CA. 14 HR WITH ONLY 2-FOLD MOLAR EXCESS OF FMOC-STATINE. THE COMPLETENESS OF THE COUPLING WAS CONFIRMED BY THE NINHYDRIN TEST. AFTER CLEAVAGE OF THE PEPTIDE FROM THE RESIN, THE CRUDE PRODUCT WAS PURIFIED BY SEMIPREPARATIVE RP-HPLC.

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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: 2.8 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG8000, PEG300, DTT and Sodium Acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 24654 / Num. obs: 24654 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.55 % / Rsym value: 0.089 / Net I/σ(I): 21.7
Reflection shellResolution: 2.6→2.63 Å / Redundancy: 3.53 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2127 / Rsym value: 0.304 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIVPR, pdb entry 1nh0

1nh0


Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.634 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS RESTRAINTS STATISTICS reported in remark 3 corresponds to conformation A of chain J in the coordinates. NCS RESTRAINTS STATISTICS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS RESTRAINTS STATISTICS reported in remark 3 corresponds to conformation A of chain J in the coordinates. NCS RESTRAINTS STATISTICS reported in remark 7 corresponds to conformation B of chain J in the coordinates.
RfactorNum. reflection% reflectionSelection details
Rfree0.27835 1143 4.7 %RANDOM
Rwork0.19833 ---
obs0.20225 23030 97.56 %-
all-24654 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.35 Å2
2---0.85 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5515 0 10 172 5697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225714
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.9997838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2025714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27324.536194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86615932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281530
X-RAY DIFFRACTIONr_chiral_restr0.1260.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024112
X-RAY DIFFRACTIONr_nbd_refined0.2550.22337
X-RAY DIFFRACTIONr_nbtor_refined0.3210.23774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.214
X-RAY DIFFRACTIONr_mcbond_it1.1151.53783
X-RAY DIFFRACTIONr_mcangle_it1.85226096
X-RAY DIFFRACTIONr_scbond_it2.45632106
X-RAY DIFFRACTIONr_scangle_it3.8594.51726
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
31I67tight positional0.080.05
32J67tight positional0.060.05
33K67tight positional0.060.05
11A883medium positional0.410.5
12C883medium positional0.430.5
13E883medium positional0.420.5
21B883medium positional0.50.5
22D883medium positional0.540.5
23F883medium positional0.550.5
31I67tight thermal0.210.5
32J67tight thermal0.160.5
33K67tight thermal0.180.5
11A883medium thermal1.42
12C883medium thermal1.472
13E883medium thermal1.222
21B883medium thermal1.192
22D883medium thermal2.242
23F883medium thermal1.512
LS refinement shellResolution: 2.601→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 52 -
Rwork0.261 1244 -
obs--75 %

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