[English] 日本語
Yorodumi
- PDB-4qj2: Crystal structure of inactive HIV-1 protease variant (I50V/A71V) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qj2
TitleCrystal structure of inactive HIV-1 protease variant (I50V/A71V) in complex with WT p1-p6 substrate
Components
  • Protease
  • p1-p6 peptide
KeywordsHYDROLASE / co-evolution / protease
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral nucleocapsid / aspartic-type endopeptidase activity / viral translational frameshifting / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protease / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLin, K.H. / Schiffer, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease.
Authors: Ozen, A. / Lin, K.H. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease
B: Protease
C: Protease
D: Protease
F: p1-p6 peptide
G: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9459
Polymers45,6626
Non-polymers2833
Water4,954275
1
A: Protease
B: Protease
G: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0195
Polymers22,8313
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-28 kcal/mol
Surface area9660 Å2
MethodPISA
2
C: Protease
D: Protease
F: p1-p6 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9264
Polymers22,8313
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-48 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.185, 63.341, 58.769
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCDFG

#1: Protein
Protease


Mass: 10828.831 Da / Num. of mol.: 4 / Mutation: Q7K, N25D, I50V, A71V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): Tap106 / References: UniProt: O38710
#2: Protein/peptide p1-p6 peptide


Mass: 1173.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04591*PLUS

-
Non-polymers , 4 types, 278 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.1 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: ammonium sulfate, sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. all: 69174 / Num. obs: 20171 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.033 / Net I/σ(I): 27.39
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 8.46 / Num. unique all: 1987 / Rsym value: 0.086 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→24.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.482 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23841 1026 5.1 %RANDOM
Rwork0.18349 ---
obs0.18626 19120 94.19 %-
all-69174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.48 Å2
2--0.22 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.13→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 16 275 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193286
X-RAY DIFFRACTIONr_bond_other_d0.0010.023374
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.994459
X-RAY DIFFRACTIONr_angle_other_deg0.75237764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47624.701117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69415591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8411518
X-RAY DIFFRACTIONr_chiral_restr0.080.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_mcbond_it0.751.5221673
X-RAY DIFFRACTIONr_mcbond_other0.751.5211672
X-RAY DIFFRACTIONr_mcangle_it1.2652.2742086
X-RAY DIFFRACTIONr_mcangle_other1.2652.2762087
X-RAY DIFFRACTIONr_scbond_it0.7551.6451613
X-RAY DIFFRACTIONr_scbond_other0.7551.6451613
X-RAY DIFFRACTIONr_scangle_other1.1722.4252374
X-RAY DIFFRACTIONr_long_range_B_refined4.53412.7793538
X-RAY DIFFRACTIONr_long_range_B_other4.53412.7853539
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 67 -
Rwork0.199 1341 -
obs-1987 87.29 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8190.0631-3.55975.0672-2.030711.38450.07880.1828-0.2079-0.1227-0.09440.15970.1787-0.43690.01560.0395-0.007-0.02950.1049-0.020.0784-32.1657-13.54230.5652
213.961.1035-4.12590.74910.22622.67390.07920.34810.2881-0.058-0.05850.14620.0361-0.1298-0.02070.07410.0009-0.01230.0952-0.00490.1111-40.0464-6.6187-2.3567
35.73490.3853-6.67166.7598.821820.5240.16440.3919-0.21890.2663-0.82790.32850.0831-1.54690.66350.0428-0.0146-0.05320.25710.1040.4012-53.1926-3.1307-0.8957
412.0172-1.88884.64083.35541.24143.08160.08770.3899-0.4442-0.20960.02850.1865-0.02310.2075-0.11610.2049-0.0325-0.01330.07780.01110.0704-40.6876-3.227-1.0499
53.9032-2.1061.45642.1546-1.69031.34730.13360.1044-0.1976-0.0943-0.04220.13840.07430.0438-0.09140.10410.0128-0.00830.1019-0.01180.0746-38.99254.13163.0351
617.6377-5.0563-6.66559.99075.63864.14630.07080.19480.0745-0.3011-0.15730.3281-0.1605-0.10580.08650.07810.00120.00540.06780.06070.14-52.50067.8567-1.439
725.25348.4191-3.639614.2964-3.43517.71080.277-0.69670.64240.5976-0.15010.4166-0.405-0.0731-0.12690.06390.0287-0.01120.0718-0.02270.1074-50.756315.86766.0377
814.822-7.7566-3.22729.79342.92614.2329-0.2044-0.0601-0.14570.0987-0.0547-0.12450.15340.04070.2590.0829-0.00360.02220.03290.02350.0974-34.999913.75760.4226
97.26072.5917-7.27382.4087-4.07058.75330.1545-0.02570.0132-0.0193-0.10460.0593-0.0820.1183-0.04990.09920.024-0.00620.0357-0.02590.1356-46.503313.14352.5257
105.0541-3.9631-1.2520.75537.525611.0162-0.2623-0.33420.01880.36860.2924-0.0993-0.16960.0419-0.03010.03750.0031-0.00630.10.02310.0757-51.0863.78039.1444
1111.0126-0.4107-9.51223.66-5.591117.9189-0.0197-0.1046-0.8754-0.6363-0.11180.42441.05650.25260.13150.17430.0092-0.00260.0944-0.07250.3944-46.7524-8.87216.1911
127.14185.6246-4.323322.6701-5.74524.6132-0.0037-0.0813-0.27420.3729-0.05430.17340.1538-0.12120.0580.094-0.0202-0.04520.14090.01970.0562-48.71750.36289.7111
134.61210.01680.8871.2748-3.08457.668-0.06310.1233-0.12110.081-0.0145-0.0074-0.24450.20690.07760.1024-0.0348-0.00290.06980.00070.1024-41.73997.5119-3.1624
140.87831.37281.42992.17312.64888.731-0.11180.02930.0427-0.10950.00030.0791-0.57710.24170.11150.10040.0341-0.00610.0827-0.02310.1106-39.17761.24314.9329
151.67013.48520.70518.7367-6.699111.8656-0.103-0.370.08180.05150.3770.629-0.0244-0.7601-0.2740.06770.04270.04210.20970.01780.1093-41.0663-3.779511.672
1625.193-6.2546-8.14836.47062.16543.1185-0.248-0.31390.05040.36720.069-0.0578-0.05130.25140.1790.1095-0.0269-0.04010.09470.03050.1226-29.6097-9.659510.5675
178.4294-10.4854-3.431614.21752.91452.9761-0.2783-0.33380.01740.37880.2249-0.07220.13980.3250.05340.156-0.0831-0.05440.15430.01090.0615-31.1646-5.474615.1684
1817.9991-2.12920.41830.2609-0.10230.5581-0.0341-0.3150.08790.0233-0.0104-0.02110.0050.15060.04450.1377-0.0547-0.02450.11260.01350.0619-26.53182.008612.0653
1921.8825-0.6231-12.41716.77397.635917.2438-0.074-0.3539-0.40840.20140.2454-0.52560.19580.4625-0.17140.08490.017-0.01490.0311-0.02390.089-11.51-0.60926.6258
2014.07682.3882-4.06236.5593-1.17357.1036-0.02130.10160.66630.04160.1111-0.2184-0.30580.2111-0.08980.1084-0.0353-0.00560.0273-0.00380.0548-14.3513.71078.1009
214.451.46814.70571.72431.00125.2236-0.0485-0.00620.1210.1258-0.04490.096-0.09590.02270.09340.0680.0302-0.00560.0960.00640.0964-27.91-1.29853.2206
229.97553.23644.60424.6153-0.94653.7958-0.0080.01290.06630.1141-0.01950.0344-0.09440.03280.02750.1-0.01280.04560.0772-0.01520.0383-21.53232.3808-2.192
234.8907-1.4655-6.12675.83054.63429.12790.1729-0.2453-0.1819-0.22470.013-0.6988-0.32870.2832-0.18590.0876-0.02180.01380.1101-0.00390.1323-9.93566.4448-3.1716
2423.4172-3.9775.79423.6587-2.59422.30370.19120.41450.0501-0.2278-0.2367-0.09170.14620.18650.04540.11060.00530.01190.0854-0.00630.0556-15.02883.936-13.536
259.335-4.5773-8.36752.26944.10247.5039-0.0648-0.22030.15450.12990.1379-0.09640.09390.1838-0.07310.2499-0.0034-0.06270.122-0.03660.1574-30.47658.3464-7.5832
2613.7873-4.99961.10095.04130.86781.3156-0.04090.32670.5104-0.0672-0.0207-0.273-0.09910.12780.06160.07730.01280.01170.06370.01770.0363-17.41146.0515-9.325
274.93730.23465.14985.0753-5.271223.03260.13320.2642-0.2085-0.2281-0.0845-0.1140.28010.0888-0.04870.06540.00040.00150.0611-0.00490.1165-11.92-4.9335-4.1656
2811.16510.7231-5.48269.058-0.41668.20540.2702-0.89070.35080.38570.3002-0.34270.23560.3555-0.57050.1185-0.0034-0.02650.1135-0.01660.08-14.83-8.56347.6263
290.0101-0.002-0.0860.00630.08871.6086-0.03630.01550.00530.00490.00070.00420.21350.03910.03570.1071-0.0197-0.010.07170.0020.131-16.1009-1.6445-3.9266
301.62383.7794-1.06399.8615-4.31883.93390.0830.00510.23680.4610.06020.5766-0.4216-0.1303-0.14320.11510.02370.02990.0469-0.01290.1767-22.70725.62691.4295
310.81-0.1846-1.01366.6314-1.86311.9352-0.03650.0299-0.07470.1544-0.1455-0.26490.00150.01820.1820.05850.01750.00460.1104-0.010.0919-22.8689-8.6639-0.0837
325.15-2.8536-7.65743.74842.417412.9255-0.25440.3255-0.27140.0779-0.1340.12720.3856-0.54160.38840.0962-0.01560.0080.08310.01190.1305-32.9041-11.88687.2297
330.88931.44142.64032.45184.32397.8605-0.41240.22360.2036-0.16740.05540.2345-0.63110.61620.35710.4914-0.3174-0.17420.21160.13370.3992-50.391722.543232.7398
3415.0007-1.00372.55020.213-1.00935.3356-0.17270.25560.6867-0.00090.0351-0.0544-0.0529-0.13830.13760.1606-0.03360.01340.06720.00540.1204-45.344717.03926.5355
3520.7825-8.175-5.45886.9286-0.526710.00140.1534-0.40.2695-0.1883-0.0715-0.4206-0.03230.4238-0.08190.0696-0.0531-0.01570.14-0.01970.1038-30.346511.121929.162
3621.9668-1.2473-8.19160.2819-0.32155.98760.26580.30850.69970.0429-0.0608-0.0551-0.3230.0271-0.2050.202-0.04520.01310.07750.01840.0843-39.261913.102327.28
375.86430.71790.07193.75190.28840.0296-0.09490.3630.09310.26470.0318-0.63670.0321-0.02370.06310.1052-0.01290.00170.1117-0.01980.1837-48.17985.246934.6771
388.21720.3731-8.25653.88083.484324.2546-0.26060.2618-0.0794-0.25540.23910.158-0.1402-0.02870.02150.0637-0.0061-0.02440.03680.00670.0702-38.35743.297126.5177
391.3750.81372.45715.4414-4.829912.54080.11390.0486-0.2713-0.16290.1502-0.23870.22230.1991-0.2640.1218-0.0775-0.03260.2420.02830.1527-28.3377-0.539530.2144
4025.48782.64783.84173.66411.052.5750.1643-0.6991-0.04280.4411-0.0583-0.0890.2139-0.0367-0.1060.12410.0095-0.01330.04050.00070.087-36.9589-8.254632.0729
4112.32-4.47823.27616.09760.06071.62270.02190.02510.074-0.29390.00470.0055-0.2367-0.1588-0.02660.12940.0208-0.0060.13550.02220.0793-49.649-3.874826.7747
427.74662.862.73371.07211.01680.96870.14070.1738-0.20660.0682-0.0173-0.08590.05920.0441-0.12350.1025-0.00570.00010.10380.00680.0846-36.2161-4.522430.0722
433.31510.26220.97571.3151.9723.0617-0.2124-0.04130.1870.28550.1351-0.01720.360.08570.07730.23730.01690.00930.09430.01170.0862-32.81827.507636.8647
4415.6565-5.32964.750411.88134.81375.55050.12070.59161.1274-0.1733-0.542-0.1611-0.0240.00360.42130.0595-0.0472-0.0240.13410.09070.3418-35.156516.489737.8173
451.99820.19380.89120.02590.18262.41890.0542-0.0748-0.2159-0.00450.0449-0.0238-0.00820.0744-0.09920.0915-0.00720.00080.1132-0.00930.0789-36.97851.537732.2977
461.5515-0.17180.84694.0631-1.48720.9475-0.1723-0.08780.0958-0.25830.13970.1079-0.0236-0.11170.03260.14260.0546-0.02320.1552-0.01240.0896-43.1636.570526.9387
475.01591.24292.58996.08584.81274.35090.0121-0.1412-0.1071-0.30010.1246-0.1909-0.21770.0319-0.13670.0799-0.0010.00750.10410.02950.0771-42.72199.383340.4319
4824.6202-12.195413.02338.5148-6.92086.9786-0.4422-0.32950.02070.21430.42820.0169-0.2417-0.22760.0140.14120.0133-0.01910.1225-0.06210.0889-53.195117.13141.0646
494.5479-8.63172.199416.4356-4.23621.1876-0.4789-0.1429-0.27631.160.33550.4475-0.3753-0.10270.14350.26460.0447-0.0690.184-0.03660.3477-51.733812.236145.0531
5012.8885-2.7593-0.11061.3451-0.79020.8808-0.0915-0.315-0.3822-0.12090.1580.17590.1692-0.067-0.06640.1462-0.01180.01950.12790.02020.1054-57.63665.708540.9131
5116.919314.11115.31116.3931-3.221314.32620.3373-0.40790.41840.3772-0.08130.5876-0.0747-0.5396-0.2560.1012-0.00480.05590.0972-0.03110.1386-72.57917.881335.1313
5217.24652.9577-0.1810.51360.00151.48390.0628-0.6032-0.06480.0449-0.1015-0.00710.23140.13060.03870.18660.0060.01430.08720.01490.0546-63.62225.704937.0161
530.621.97960.06796.3567-0.05162.1048-0.11970.0580.0099-0.29580.13120.02770.17390.0789-0.01150.0654-0.0238-0.00630.1309-0.0210.0585-56.46810.042827.6225
5411.60682.2831-4.04364.4430.12666.65040.06830.2012-0.2630.1834-0.20750.12330.70430.2110.13920.19890.0009-0.02680.06620.01290.056-68.75220.810627.3302
556.55792.6784-4.19394.08242.647420.9484-0.16990.23870.2953-0.2670.05610.0375-0.1961-0.54240.11380.03860.0204-0.02560.06670.00160.0872-73.96327.25219.0015
5619.2485-2.84946.72390.66610.23758.5744-0.14980.5291.1028-0.0147-0.0954-0.1955-0.25210.01380.24520.11010.00650.04470.08630.0390.1477-62.29445.335515.3777
574.40851.67544.56745.8862-1.0036.16110.01460.2758-0.05050.3465-0.0838-0.2395-0.16850.38970.06930.11150.02130.00880.09460.01220.09-52.69140.498220.6558
589.0842-5.92792.180910.8385-0.84943.79840.11280.2967-0.0329-0.1175-0.04-0.17110.1635-0.1971-0.07280.0388-0.0308-0.01060.0972-0.02310.0358-67.08195.747519.0348
5911.0015-1.77844.9155.3487-1.28236.1880.1442-0.05620.09690.21650.11770.2331-0.4098-0.002-0.26190.0455-0.01020.01980.0107-0.00320.1244-70.957914.272229.4929
6010.5504-7.7616-3.112719.226210.07045.5092-0.1207-1.13010.58560.49250.5034-0.52960.20190.1797-0.38260.1672-0.0020.01530.2494-0.06750.1798-67.335217.222537.1865
614.0001-1.3166-0.8160.71431.0452.3246-0.0011-0.00060.2708-0.06640.0649-0.1029-0.19170.0635-0.06380.094-0.0184-0.0120.1104-0.00450.0586-66.3179.811824.5968
623.7532-1.3306-0.49173.71895.510513.2097-0.0149-0.1633-0.13940.22960.0924-0.28410.3950.4468-0.07750.0983-0.0083-0.01980.07720.01780.1101-60.18610.898729.5425
634.0907-3.08650.33615.34340.11940.0738-0.0783-0.13660.20650.12020.01960.18150.0003-0.02480.05860.06040.0103-0.01520.1126-0.01360.0727-59.763816.592830.8333
6413.95770.591315.8221.06833.077423.5168-0.36640.410.7682-0.0970.0926-0.234-0.67290.64160.27380.1814-0.0365-0.0390.1059-0.05840.1721-48.953419.495738.1418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 13
3X-RAY DIFFRACTION3A14 - 19
4X-RAY DIFFRACTION4A20 - 25
5X-RAY DIFFRACTION5A26 - 34
6X-RAY DIFFRACTION6A35 - 39
7X-RAY DIFFRACTION7A40 - 44
8X-RAY DIFFRACTION8A45 - 54
9X-RAY DIFFRACTION9A55 - 59
10X-RAY DIFFRACTION10A60 - 64
11X-RAY DIFFRACTION11A65 - 69
12X-RAY DIFFRACTION12A70 - 75
13X-RAY DIFFRACTION13A76 - 82
14X-RAY DIFFRACTION14A83 - 88
15X-RAY DIFFRACTION15A89 - 94
16X-RAY DIFFRACTION16A95 - 99
17X-RAY DIFFRACTION17B1 - 6
18X-RAY DIFFRACTION18B7 - 11
19X-RAY DIFFRACTION19B12 - 17
20X-RAY DIFFRACTION20B18 - 22
21X-RAY DIFFRACTION21B23 - 28
22X-RAY DIFFRACTION22B29 - 34
23X-RAY DIFFRACTION23B35 - 39
24X-RAY DIFFRACTION24B40 - 46
25X-RAY DIFFRACTION25B47 - 53
26X-RAY DIFFRACTION26B54 - 59
27X-RAY DIFFRACTION27B60 - 64
28X-RAY DIFFRACTION28B65 - 70
29X-RAY DIFFRACTION29B71 - 78
30X-RAY DIFFRACTION30B79 - 86
31X-RAY DIFFRACTION31B87 - 93
32X-RAY DIFFRACTION32B94 - 99
33X-RAY DIFFRACTION33C1 - 6
34X-RAY DIFFRACTION34C7 - 12
35X-RAY DIFFRACTION35C13 - 18
36X-RAY DIFFRACTION36C19 - 24
37X-RAY DIFFRACTION37C25 - 30
38X-RAY DIFFRACTION38C31 - 35
39X-RAY DIFFRACTION39C36 - 41
40X-RAY DIFFRACTION40C42 - 46
41X-RAY DIFFRACTION41C47 - 54
42X-RAY DIFFRACTION42C55 - 59
43X-RAY DIFFRACTION43C60 - 66
44X-RAY DIFFRACTION44C67 - 71
45X-RAY DIFFRACTION45C72 - 79
46X-RAY DIFFRACTION46C80 - 86
47X-RAY DIFFRACTION47C87 - 94
48X-RAY DIFFRACTION48C95 - 99
49X-RAY DIFFRACTION49D1 - 6
50X-RAY DIFFRACTION50D7 - 12
51X-RAY DIFFRACTION51D13 - 18
52X-RAY DIFFRACTION52D19 - 24
53X-RAY DIFFRACTION53D25 - 32
54X-RAY DIFFRACTION54D33 - 37
55X-RAY DIFFRACTION55D38 - 42
56X-RAY DIFFRACTION56D43 - 47
57X-RAY DIFFRACTION57D48 - 54
58X-RAY DIFFRACTION58D55 - 60
59X-RAY DIFFRACTION59D61 - 65
60X-RAY DIFFRACTION60D66 - 71
61X-RAY DIFFRACTION61D72 - 78
62X-RAY DIFFRACTION62D79 - 84
63X-RAY DIFFRACTION63D85 - 94
64X-RAY DIFFRACTION64D95 - 99

+
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://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