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- PDB-8eri: HTLV-1 capsid protein full-length -

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Basic information

Entry
Database: PDB / ID: 8eri
TitleHTLV-1 capsid protein full-length
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 / Retroviral nucleocapsid Gag protein p24, N-terminal / 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 ...Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / 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: 2.25 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 full-length
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
C: capsid protein p24


Theoretical massNumber of molelcules
Total (without water)71,3943
Polymers71,3943
Non-polymers00
Water1,74797
1
A: capsid protein p24


Theoretical massNumber of molelcules
Total (without water)23,7981
Polymers23,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: capsid protein p24


Theoretical massNumber of molelcules
Total (without water)23,7981
Polymers23,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: capsid protein p24


Theoretical massNumber of molelcules
Total (without water)23,7981
Polymers23,7981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.079, 128.663, 297.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein capsid protein p24 /


Mass: 23798.004 Da / Num. of mol.: 3
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: U3RC60
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M Na citrate, pH 6.0 8% 2-propanol 23% PEG3350

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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: Jul 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→48.64 Å / Num. obs: 33745 / % possible obs: 99.4 % / Redundancy: 13.5 % / Biso Wilson estimate: 43.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.04 / Rrim(I) all: 0.148 / Net I/σ(I): 8.5 / Num. measured all: 454329 / Scaling rejects: 7
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
2.25-2.3212.81.2223696228770.8230.3461.2711.293.2
9-48.6412.40.07973795930.9970.0220.08325.299.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.47 Å48.01 Å
Translation1.47 Å48.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.8data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 prediction

Resolution: 2.25→43.63 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1771 5.26 %
Rwork0.2508 31927 -
obs0.2528 33698 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 400.64 Å2 / Biso mean: 118.9821 Å2 / Biso min: 29.08 Å2
Refinement stepCycle: final / Resolution: 2.25→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 0 97 4927
Biso mean---57.86 -
Num. residues----618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.39941350.34912207234291
2.31-2.380.38051270.315324542581100
2.38-2.450.35531360.312224232559100
2.45-2.540.28491260.307624522578100
2.54-2.640.31421450.274824622607100
2.64-2.760.26261290.24724452574100
2.76-2.910.25431510.242124392590100
2.91-3.090.29761320.275724892621100
3.09-3.330.27811380.247924622600100
3.33-3.670.29761430.235124612604100
3.67-4.20.24981310.23324942625100
4.2-5.290.28351390.220725382677100
5.29-43.630.28941390.250126012740100
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)
13.88950.10232.82915.9664-0.96253.64540.0149-0.3591-0.64140.04580.06550.35151.2708-1.0417-0.11150.22750.00980.08290.37870.02290.7307-5.8075-21.412952.7582
22.50850.57571.93413.07730.45765.3739-0.20670.04730.566-0.1179-0.08-0.0694-0.2970.2380.24990.26430.01270.03360.26420.04310.64333.6382-11.182454.9224
35.10290.9827-0.45712.4946-0.26023.9710.0665-0.4699-1.37120.0931-0.26870.26870.66150.06030.17540.60230.0689-0.2206-0.0175-0.0202-0.1236-4.3163-6.65325.1013
43.39942.82431.21539.0116-4.00056.5285-0.57330.65630.24310.31751.22610.8792-2.32681.352-0.93242.6406-0.2075-0.54311.7739-0.00741.661-10.7435-0.425812.6767
52.6129-0.14640.52092.89811.71125.0045-0.0166-0.05880.0705-0.0518-0.06330.1665-0.1421-0.04840.10140.2003-0.0088-0.01780.27260.05460.6629-24.5018-5.946654.2999
60.6367-0.66490.34431.8109-0.68228.52540.31040.9707-0.6619-0.7659-0.1205-0.22940.461-0.3273-0.20011.08880.1441-0.04821.4759-0.3390.5694-36.3064-7.861419.9647
73.0016-0.7605-1.48732.54791.51875.7143-0.12890.0916-0.32220.00920.01820.14630.0673-0.16640.12030.2627-0.0169-0.04080.21170.01220.6132-44.0943-24.212954.3851
86.90440.0153.18977.92811.95128.307-0.12131.6606-0.446-1.41520.4711-2.1220.57430.4519-0.04831.1357-0.28480.19221.2694-0.15650.8752-48.1339-36.005320.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )A1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 123 )A35 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 175 )A124 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 207 )A176 - 207
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 123 )B1 - 123
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 207 )B124 - 207
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 123 )C1 - 123
8X-RAY DIFFRACTION8chain 'C' and (resid 124 through 207 )C124 - 207

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