[English] 日本語
Yorodumi
- PDB-6oc8: Crystal structure of a VHH against the capsid protein from BLV -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.42 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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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