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- PDB-6oc8: Crystal structure of a VHH against the capsid protein from BLV -

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Basic information

Entry
Database: PDB / ID: 6oc8
TitleCrystal structure of a VHH against the capsid protein from BLV
ComponentsVHH8c
KeywordsIMMUNE SYSTEM / VHH heavy chain antibody / BLV capsid protein
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.109 Å
AuthorsCarrion, F. / Larrieux, N. / Trajtenberg, F. / Buschiazzo, A.
CitationJournal: To be Published
Title: BLV capsid self-assembly inhibition by heavy chain antibodies
Authors: Carrion, F. / Larrieux, N. / Trajtenberg, F. / Gonzalez-Sapienza, G. / Buschiazzo, A. / Pritsch, O.
History
DepositionMar 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VHH8c
B: VHH8c
C: VHH8c
D: VHH8c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50714
Polymers52,5504
Non-polymers95710
Water68538
1
A: VHH8c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4264
Polymers13,1381
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VHH8c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3303
Polymers13,1381
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VHH8c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4224
Polymers13,1381
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VHH8c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3303
Polymers13,1381
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.560, 120.720, 69.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 5 or (resid 6...
21(chain B and (resid 4 through 7 or (resid 8...
31(chain C and (resid 4 through 23 or resid 25...
41(chain D and (resid 4 through 23 or resid 25...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 4 through 5 or (resid 6...AA4 - 54 - 5
12GLUGLUGLUGLU(chain A and (resid 4 through 5 or (resid 6...AA66
13METMETSERSER(chain A and (resid 4 through 5 or (resid 6...AA4 - 1244 - 124
14METMETSERSER(chain A and (resid 4 through 5 or (resid 6...AA4 - 1244 - 124
15METMETSERSER(chain A and (resid 4 through 5 or (resid 6...AA4 - 1244 - 124
16METMETSERSER(chain A and (resid 4 through 5 or (resid 6...AA4 - 1244 - 124
21METMETVALVAL(chain B and (resid 4 through 7 or (resid 8...BB4 - 74 - 7
22GLNGLNGLNGLN(chain B and (resid 4 through 7 or (resid 8...BB88
23HISHISSERSER(chain B and (resid 4 through 7 or (resid 8...BB3 - 1253 - 125
24HISHISSERSER(chain B and (resid 4 through 7 or (resid 8...BB3 - 1253 - 125
25HISHISSERSER(chain B and (resid 4 through 7 or (resid 8...BB3 - 1253 - 125
31METMETLEULEU(chain C and (resid 4 through 23 or resid 25...CC4 - 234 - 23
32LEULEUGLNGLN(chain C and (resid 4 through 23 or resid 25...CC25 - 4425 - 44
33THRTHRTHRTHR(chain C and (resid 4 through 23 or resid 25...CC4545
34METMETSERSER(chain C and (resid 4 through 23 or resid 25...CC4 - 1254 - 125
35METMETSERSER(chain C and (resid 4 through 23 or resid 25...CC4 - 1254 - 125
36METMETSERSER(chain C and (resid 4 through 23 or resid 25...CC4 - 1254 - 125
37METMETSERSER(chain C and (resid 4 through 23 or resid 25...CC4 - 1254 - 125
41METMETLEULEU(chain D and (resid 4 through 23 or resid 25...DD4 - 234 - 23
42LEULEUGLNGLN(chain D and (resid 4 through 23 or resid 25...DD25 - 4425 - 44
43METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123
44METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123
45METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123
46METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123
47METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123
48METMETVALVAL(chain D and (resid 4 through 23 or resid 25...DD4 - 1234 - 123

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Components

#1: Protein
VHH8c


Mass: 13137.548 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.00 M ammonium sulfate, 7% isopropanol, 15% pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2015 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
Reflection twinOperator: -k,h,l / Fraction: 0.48
ReflectionResolution: 2.11→60.36 Å / Num. obs: 29590 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.065 / Rrim(I) all: 0.153 / Net I/σ(I): 8.7 / Num. measured all: 152335 / Scaling rejects: 6
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
2.11-2.225.30.6662255442800.7620.3150.742.399.9
6.67-60.364.80.056485310190.9970.0270.06320.298.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XT1

4xt1


Resolution: 2.109→60.36 Å / Cross valid method: THROUGHOUT / σ(F): 34.48 / Phase error: 26.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2407 1567 5.3 %
Rwork0.2053 28008 -
obs0.2107 29584 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.45 Å2 / Biso mean: 28.4875 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: final / Resolution: 2.109→60.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 51 38 3602
Biso mean--48.33 17.45 -
Num. residues----486
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1432X-RAY DIFFRACTION4.25TORSIONAL
12B1432X-RAY DIFFRACTION4.25TORSIONAL
13C1432X-RAY DIFFRACTION4.25TORSIONAL
14D1432X-RAY DIFFRACTION4.25TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1085-2.17650.28681260.2412554268095
2.1765-2.25430.27761380.24152544268295
2.2543-2.34450.26981420.2382515265795
2.3445-2.45110.28021430.23862537268094
2.4511-2.58030.25661440.22872536268094
2.5803-2.74180.28221410.21972536267794
2.7418-2.95320.31951570.22252531268894
2.9532-3.250.24121330.20892562269595
3.25-3.71920.24771490.19432448259790
3.7192-4.68180.20791480.17662564271293
4.6818-26.98880.20481380.19842681281994
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)
11.2113-0.5306-0.42451.6215-0.33880.6353-0.0343-0.04870.3453-0.19050.03010.0725-0.03870.0041-0.0110.15390.0034-0.09430.1021-0.02250.455113.6113-19.6504-18.226
20.9860.17590.36921.9887-0.59931.16510.0099-0.03070.0249-0.0420.0250.4379-0.0724-0.0436-0.01170.16540.01150.03870.0881-0.02380.330417.0262-49.3594-18.3948
31.16760.6390.23772.86681.44832.0403-0.00750.05970.0551-0.08960.0376-0.2345-0.0250.0816-0.01970.1640.00820.0180.06920.02520.267543.3756-16.1532-17.4686
41.3405-0.44440.69241.7918-0.33281.26920.0890.0635-0.17550.0131-0.1648-0.24470.26090.06070.02850.1891-0.01240.02980.10850.01160.429246.8803-45.8695-18.0496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 4:124)A4 - 124
2X-RAY DIFFRACTION2(chain B and resseq 3:125)B3 - 125
3X-RAY DIFFRACTION3(chain C and resseq 4:125)C4 - 125
4X-RAY DIFFRACTION4(chain D and resseq 4:123)D4 - 123

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