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- PDB-8erh: HTLV-1 capsid protein C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8erh
TitleHTLV-1 capsid protein C-terminal domain
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: 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 C-terminal domain
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

Downloads & links

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Assembly

Deposited unit
A: capsid protein p24
B: capsid protein p24
C: capsid protein p24
D: capsid protein p24
E: capsid protein p24
F: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,69113
Polymers58,0266
Non-polymers6657
Water9,440524
1
A: capsid protein p24
B: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6275
Polymers19,3422
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-25 kcal/mol
Surface area9750 Å2
MethodPISA
2
C: capsid protein p24
D: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5324
Polymers19,3422
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-18 kcal/mol
Surface area9140 Å2
MethodPISA
3
E: capsid protein p24
F: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5324
Polymers19,3422
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-23 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.982, 94.121, 96.020
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: 9670.993 Da / Num. of mol.: 6
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: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 1.5 M (NH4)2SO4, 0.1 M Na2HPO4, pH 4.2

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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→49 Å / Num. obs: 88526 / % possible obs: 99.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 19.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Net I/σ(I): 15.4 / Num. measured all: 1179696 / Scaling rejects: 186
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
1.47-1.4912.11.3324833439900.6880.3861.391.492.1
8.04-4911.20.03770526310.9990.0110.0384598.9

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

Resolution: 1.47→36.72 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 4387 4.97 %
Rwork0.1679 83829 -
obs0.1691 88216 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.45 Å2 / Biso mean: 30.3468 Å2 / Biso min: 9.96 Å2
Refinement stepCycle: final / Resolution: 1.47→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 35 524 4348
Biso mean--30.95 34.77 -
Num. residues----488
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 (%)
1.47-1.480.33131120.31342278239082
1.48-1.50.23351510.243927692920100
1.5-1.520.22581690.231727672936100
1.52-1.540.25781480.215627762924100
1.54-1.560.23241410.209127512892100
1.56-1.580.23211630.204727832946100
1.58-1.60.24361560.195927832939100
1.6-1.630.22271510.188827832934100
1.63-1.650.21560.181527282884100
1.65-1.680.22751560.172328222978100
1.68-1.710.20791260.176327782904100
1.71-1.740.19181600.183727922952100
1.74-1.770.21071480.17727812929100
1.77-1.810.19181160.174527982914100
1.81-1.850.21211300.172328272957100
1.85-1.890.20231560.167328082964100
1.89-1.940.19681380.166127682906100
1.94-1.990.23051800.168327712951100
1.99-2.050.18021510.164928062957100
2.05-2.120.18231350.156228132948100
2.12-2.190.17451240.155128412965100
2.19-2.280.18961380.147328422980100
2.28-2.380.15691550.148927912946100
2.38-2.510.20111480.154328082956100
2.51-2.670.18371490.16428442993100
2.67-2.870.17921300.163328482978100
2.87-3.160.17881470.161128673014100
3.16-3.620.15671520.14828723024100
3.62-4.560.16091620.146428863048100
4.56-36.720.2531390.205930483187100
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)
12.1651-0.35571.13752.7089-0.96633.2385-0.0533-0.13440.07630.12750.03380.1698-0.138-0.12330.030.10750.0270.03510.1357-0.01140.13375.0478-10.089317.3834
23.30740.4186-0.08864.54710.21652.4091-0.0240.00120.2341-0.2892-0.0105-0.181-0.25110.04940.01980.1618-0.009-0.00630.10930.0060.1103-9.760521.68667.3028
32.5351-0.0822-0.93733.7391.08532.94980.0411-0.14050.05020.0498-0.0273-0.22190.09690.00920.00480.11580.0015-0.02450.12270.00020.1092-4.175310.534618.4739
43.04390.11990.29753.63930.0832.4827-0.0539-0.0035-0.17570.0041-0.00510.05290.17780.03370.04260.11070.01510.02940.1172-0.01280.115913.2211-21.17227.8053
52.35620.53280.31293.49990.55332.83060.0185-0.0001-0.08780.0292-0.0469-0.00420.1129-0.01560.02030.09610.0102-0.00070.10510.00110.102236.1593-5.49634.3223
63.93680.9085-0.37773.4282-0.84492.7364-0.0135-0.00810.1341-0.0421-0.02810.0679-0.05970.03670.01150.09060.0181-0.00810.11320.01790.124723.84244.86690.7551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 128 through 207)C128 - 207
2X-RAY DIFFRACTION2(chain 'A' and resid 128 through 207)A128 - 207
3X-RAY DIFFRACTION3(chain 'B' and resid 128 through 207)B128 - 207
4X-RAY DIFFRACTION4(chain 'D' and resid 128 through 207)D128 - 207
5X-RAY DIFFRACTION5(chain 'E' and resid 128 through 207)E128 - 207
6X-RAY DIFFRACTION6(chain 'F' and resid 128 through 207)F128 - 207

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