[English] 日本語
Yorodumi
- PDB-3lzu: Crystal Structure of a Nelfinavir Resistant HIV-1 CRF01_AE Protea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lzu
TitleCrystal Structure of a Nelfinavir Resistant HIV-1 CRF01_AE Protease variant (N88S) in Complex with the Protease Inhibitor Darunavir.
ComponentsHIV-1 protease
KeywordsHYDROLASE / HIV-1 protease / non-B clades / CRF01_AE / inhibitor resistance / AIDS / Aspartyl protease
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / 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 / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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
Chem-017 / ACETATE ION / Gag-Pol polyprotein / HIV-1 protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsSchiffer, C.A. / Bandaranayake, R.M.
CitationJournal: J.Virol. / Year: 2010
Title: The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways.
Authors: Bandaranayake, R.M. / Kolli, M. / King, N.M. / Nalivaika, E.A. / Heroux, A. / Kakizawa, J. / Sugiura, W. / Schiffer, C.A.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: HIV-1 protease
A: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3228
Polymers21,4802
Non-polymers8436
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.878, 61.878, 82.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein HIV-1 protease


Mass: 10739.773 Da / Num. of mol.: 2 / Mutation: Q7K, N88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NH1 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106
References: UniProt: Q9QB59, UniProt: P24740*PLUS, HIV-1 retropepsin
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2008 / Details: bent conical Si, Rh coating
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.76→53.61 Å / Num. all: 79445 / % possible obs: 97.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.041 / Χ2: 0.982 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.76-1.822.60.40114080.73179.4
1.82-1.940.31117290.75399.1
1.9-1.984.80.21717741.07299.8
1.98-2.094.90.14217561.05399.9
2.09-2.224.90.117631.06499.9
2.22-2.394.90.08517781.09399.9
2.39-2.634.90.05217540.988100
2.63-3.014.90.03817820.972100
3.01-3.794.90.03717820.9499.9
3.79-504.70.02717510.92996.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
BioCARSsoftwaredata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TSU

1tsu


Resolution: 1.76→53.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.217 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.827 / SU B: 4.948 / SU ML: 0.1 / SU R Cruickshank DPI: 0.149 / SU Rfree: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 872 5.1 %RANDOM
Rwork0.196 ---
obs0.198 -98 %-
all-79445 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.7 Å2 / Biso mean: 33.054 Å2 / Biso min: 18.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.76→53.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 58 81 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221584
X-RAY DIFFRACTIONr_bond_other_d0.0020.021051
X-RAY DIFFRACTIONr_angle_refined_deg1.72.0512155
X-RAY DIFFRACTIONr_angle_other_deg0.89932594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.25196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82925.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.27156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.210.2247
X-RAY DIFFRACTIONr_nbd_other0.2060.21112
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2733
X-RAY DIFFRACTIONr_nbtor_other0.0880.2880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.25
X-RAY DIFFRACTIONr_mcbond_it1.2071.51265
X-RAY DIFFRACTIONr_mcbond_other0.2531.5414
X-RAY DIFFRACTIONr_mcangle_it1.40321586
X-RAY DIFFRACTIONr_scbond_it2.2273680
X-RAY DIFFRACTIONr_scangle_it2.9094.5569
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 47 -
Rwork0.267 1007 -
all-1054 -
obs--81.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4094-0.13378.30796.3221-4.759516.424-0.01620.1604-0.7332-0.20150.0206-0.25441.0310.101-0.0045-0.08220.00530.0532-0.1308-0.0215-0.077816.6973-32.3545-0.7123
26.32571.34160.3278.39667.224118.08260.0732-0.1856-0.7484-0.1639-0.0775-0.56990.58430.8170.0043-0.13330.02620.0153-0.120.0492-0.053219.6261-30.63720.9666
312.3622-3.3305-20.378512.83512.236244.02120.33190.91520.0879-0.4225-0.02490.3625-0.3719-1.6467-0.307-0.0471-0.102-0.04950.0193-0.0249-0.10456.9405-28.5545-5.9919
48.36141.5311-4.053714.2368-19.384341.74230.258-0.41930.44160.8545-0.2834-0.3219-1.45140.94590.0254-0.1374-0.0934-0.07010.052-0.0194-0.13821.799-20.27056.4698
54.52641.3066-3.41242.8919-2.05683.0294-0.0767-0.33040.20860.14470.0799-0.0213-0.090.2427-0.0032-0.0917-0.06340.0046-0.0231-0.0351-0.09129.4813-21.70615.3022
61.85433.7439-0.54379.9253-1.033215.56550.1946-0.36560.12461.1792-0.32071.24550.1535-1.84560.12610.0598-0.02380.20610.1938-0.06540.1344-2.4312-18.834116.45
74.31211.6536-2.88823.8026-2.07093.6183-0.04260.11010.1418-0.36130.03980.2530.2686-0.19350.0027-0.1056-0.0604-0.0275-0.02240.0192-0.101214.0059-19.0251-4.9786
812.5276-1.66743.48770.2667-1.520625.9075-0.10181.04331.4163-0.1071-0.3615-0.4586-1.80661.18680.46340.0956-0.06470.0190.01150.19830.097217.5338-7.2575-15.5168
90.66862.2612-1.54419.8441-2.431230.79930.3528-0.18010.4432.1222-0.37720.39930.38710.14390.02430.0927-0.1195-0.024-0.0909-0.0580.0186.0819-8.843511.2512
100.92184.0052-2.008317.4023-8.72574.37520.54550.11980.79851.0837-1.19220.0908-0.44920.18550.64670.0809-0.03150.1314-0.02370.02150.08254.5255-8.05357.4796
1120.2733-3.9843-4.61961.3315-3.133630.83240.7491.9130.536-0.1738-0.50230.39930.21350.3292-0.2467-0.12480.0473-0.04890.0764-0.0227-0.02034.6245-9.6019-10.9775
1225.73163.1823-18.05162.1265-2.306629.2090.43221.29021.47240.52-0.17910.7934-0.7846-1.1079-0.2532-0.07540.06940.0765-0.04790.10110.0684.8145-6.1925-8.0667
136.8122-11.54952.333125.9322-4.727510.12290.0043-0.6573-0.12841.85610.14650.5378-1.2573-0.1669-0.15090.0774-0.08140.1422-0.0581-0.0731-0.16272.6325-17.706318.632
1415.870.4639-6.068111.863914.780264.4912-0.28230.8095-1.1715-0.04180.06910.0241.03480.56080.2132-0.1488-0.0506-0.0210.05710.0512-0.02434.8977-32.177212.7338
155.9941-0.74190.601323.1142-5.007810.01560.3452-0.4128-0.46360.5825-0.4483-0.65950.18870.47620.1031-0.2043-0.07140.0047-0.04640.0426-0.14397.685-27.827915.3124
1614.7028-16.1329-2.978322.70965.18129.47080.57481.32910.1026-1.2904-0.3566-0.2137-0.6971-0.9697-0.2182-0.06380.0139-0.00010.13620.1468-0.169714.1276-11.6639-18.7968
1726.6857-2.424720.644324.2555-22.325263.31680.218-0.0315-1.08740.9724-0.2694-0.93240.57780.85940.0513-0.0551-0.0850.037-0.1262-0.0633-0.045925.708-20.4091-12.7284
1817.9381-7.7314-2.961911.39963.39098.6491-0.13770.7786-0.8934-0.05530.00710.01520.3416-0.14480.1306-0.1527-0.09270.0501-0.1122-0.0052-0.151920.2627-20.5978-15.0162
194.4124-0.894-1.40738.3440.12365.0420.27710.3540.2728-0.0904-0.27920.5386-0.4967-0.18620.0021-0.1358-0.02520.0136-0.06410.0117-0.06491.5574-18.25535.551
206.426-3.58650.46975.6442-1.75644.569-0.06410.09420.59780.57820.02320.1279-0.4254-0.25270.0409-0.1115-0.05050.0202-0.0867-0.0033-0.033715.0057-10.4777-5.2682
218.7391-3.8001-5.720510.0669-8.961919.32370.2981-0.9775-0.12230.5602-0.44490.0509-0.36350.5890.1467-0.1674-0.0817-0.01670.07690.033-0.136613.7618-25.709410.5037
2213.5317-3.3011-12.14177.3690.267616.44-0.52340.9876-0.1556-0.2850.2582-0.10930.2806-0.46110.2652-0.0912-0.13350.0152-0.0553-0.0338-0.142115.3871-24.7582-10.207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION2B1 - 5
4X-RAY DIFFRACTION2B94 - 99
5X-RAY DIFFRACTION3A6 - 10
6X-RAY DIFFRACTION4B6 - 10
7X-RAY DIFFRACTION5A22 - 32
8X-RAY DIFFRACTION6A33 - 43
9X-RAY DIFFRACTION7B22 - 32
10X-RAY DIFFRACTION8B33 - 43
11X-RAY DIFFRACTION9A44 - 49
12X-RAY DIFFRACTION10A52 - 56
13X-RAY DIFFRACTION11B44 - 49
14X-RAY DIFFRACTION12B52 - 56
15X-RAY DIFFRACTION13A57 - 62
16X-RAY DIFFRACTION14A63 - 68
17X-RAY DIFFRACTION15A69 - 76
18X-RAY DIFFRACTION16B57 - 62
19X-RAY DIFFRACTION17B63 - 68
20X-RAY DIFFRACTION18B69 - 76
21X-RAY DIFFRACTION19A77 - 85
22X-RAY DIFFRACTION20B77 - 85
23X-RAY DIFFRACTION21A86 - 93
24X-RAY DIFFRACTION22B86 - 93

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more