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- PDB-8erf: HTLV-1 capsid protein N-terminal domain orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 8erf
TitleHTLV-1 capsid protein N-terminal domain orthorhombic crystal form
Componentscapsid protein p24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral process / viral nucleocapsid / nucleic acid binding / structural molecule activity / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle ...Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHTLV-1 subtype C (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsYu, R.J. / Li, N. / Jacques, D.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214344/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: HTLV-1 capsid protein N-terminal domain orthorhombic crystal form
Authors: Yu, R.J. / Li, N. / Jacques, D.A.
History
DepositionOct 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein p24
B: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3863
Polymers28,2902
Non-polymers961
Water3,945219
1
A: capsid protein p24


Theoretical massNumber of molelcules
Total (without water)14,1451
Polymers14,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2412
Polymers14,1451
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.769, 77.323, 101.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein capsid protein p24 /


Mass: 14144.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HTLV-1 subtype C (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 / References: UniProt: U3RC00
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M (NH4)SO4, 25% PEG 4000, 0.1 M Na acetate, pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→42.55 Å / Num. obs: 42553 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 15.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 15.4 / Num. measured all: 553859 / Scaling rejects: 231
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.4912.20.7132364419390.8570.210.7442.495.1
8.03-42.5510.30.04633373240.9980.0150.04836.499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.8 Å42.55 Å
Translation3.8 Å42.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 prediction

Resolution: 1.47→42.55 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 4311 10.15 %
Rwork0.1817 38154 -
obs0.1842 42465 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.28 Å2 / Biso mean: 24.1318 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.47→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 5 219 2208
Biso mean--14.51 28.69 -
Num. residues----253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.480.33551300.30151120125092
1.48-1.50.26081420.232912581400100
1.5-1.520.22311450.209612521397100
1.52-1.540.22241440.210912881432100
1.54-1.560.24471660.185111861352100
1.56-1.580.21991470.189112501397100
1.58-1.60.20331390.182712661405100
1.6-1.630.22331240.180513061430100
1.63-1.650.22211130.182812571370100
1.65-1.680.21281650.191312341399100
1.68-1.710.19111370.186412931430100
1.71-1.740.22821440.184812281372100
1.74-1.770.21261730.18412531426100
1.77-1.810.1921320.175212861418100
1.81-1.850.22421390.185312401379100
1.85-1.890.21371440.199312781422100
1.89-1.940.24871350.195512851420100
1.94-1.990.22071440.179212421386100
1.99-2.050.18971490.178212861435100
2.05-2.120.19351290.171212611390100
2.12-2.190.17121290.160313251454100
2.19-2.280.16661370.158412511388100
2.28-2.380.20091380.161113111449100
2.38-2.510.17251610.165912521413100
2.51-2.670.18531570.167112811438100
2.67-2.870.19281360.182113131449100
2.87-3.160.21291370.181813001437100
3.16-3.620.2051560.1813021458100
3.62-4.560.1941560.160913401496100
4.56-42.550.25741630.219614101573100
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)
11.855-3.0291-0.16547.3131-1.41461.2678-0.3031-0.67541.18191.05750.12650.198-0.58420.06850.0860.31040.0328-0.00820.1871-0.09730.559115.845426.468315.5098
22.35273.04611.43378.7267-4.10748.970.10570.098-0.1531-0.1147-0.0342-0.19040.32960.191-0.02830.12380.0274-0.00610.18150.00780.118622.515310.210420.9515
33.51632.2759-0.1967.4743-1.16065.4725-0.1071-0.3249-0.12420.06280.1026-0.21340.2929-0.058-0.05070.09910.053-0.01870.1928-0.00520.107811.74688.181322.8651
43.4884-0.88520.6461.3228-0.47491.45370.0070.17080.0635-0.0429-0.0095-0.04160.0454-0.0290.00410.08970.00040.00610.0923-0.00020.07986.170713.28617.3374
55.2669-0.1509-0.0977.4281-0.43943.8041-0.0286-0.1572-0.1390.18810.13530.08840.2348-0.0572-0.08990.07590.0078-0.00540.1084-0.00820.06384.415711.466414.7596
63.2254-0.7726-0.95293.4061-3.49884.5784-0.01710.5107-0.8753-1.0918-0.0601-0.11660.731-0.01320.13790.3166-0.0139-0.04280.1692-0.02970.361329.2515-2.422237.1675
73.88291.5198-4.76014.30740.22598.44070.00970.0756-0.4796-0.2462-0.2292-0.83650.19490.54090.51930.10230.0075-0.02630.15830.05480.20135.14226.348139.2714
83.0029-3.32392.46815.2078-4.55084.14740.0222-0.2763-0.2450.1774-0.1748-0.1995-0.19740.31670.08110.1544-0.0156-0.02570.21290.02980.139438.663916.065230.9517
93.7562-1.30892.56643.56383.18697.11080.20270.61931.5881-0.2757-0.1835-1.1449-1.0730.8935-0.10750.3447-0.07440.0180.22610.11330.384729.652526.534627.7684
105.3256-3.07431.80121.8259-1.0253.9640.07740.18730.2162-0.0468-0.1613-0.2051-0.2840.21490.08970.1282-0.0090.00320.13320.02260.082526.637415.859628.0435
112.73740.7667-0.52521.6950.22811.90230.1079-0.1890.2928-0.0324-0.0402-0.038-0.16250.0343-0.07050.1123-0.0157-0.00530.1123-0.00490.089822.997919.760942.1733
123.49561.0405-1.15661.2870.10823.01560.0184-0.2159-0.0950.2117-0.0380.0521-0.0774-0.1041-0.01250.1046-0.0096-0.00670.1290.00820.085418.668311.544841.6329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 27 )A17 - 27
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 48 )A28 - 48
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 106 )A49 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 127 )A107 - 127
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 10 )B1 - 10
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 16 )B11 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 26 )B17 - 26
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 34 )B27 - 34
10X-RAY DIFFRACTION10chain 'B' and (resid 35 through 48 )B35 - 48
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 85 )B49 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 126 )B86 - 126

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