[English] 日本語
Yorodumi
- PDB-7aqz: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aqz
TitleCo-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB14)
Components
  • Nanobody VSG2(NB14)
  • Variant surface glycoprotein MITAT 1.2
KeywordsMEMBRANE PROTEIN / Variant surface Glycoprotein / Epitope Mapping / Immune Evasion
Function / homology
Function and homology information


symbiont-mediated evasion of host immune response / side of membrane / plasma membrane
Similarity search - Function
Variant surface glycoprotein C-terminal domain superfamily / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Variant surface glycoprotein MITAT 1.2
Similarity search - Component
Biological speciesLama glama (llama)
Trypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsStebbins, C.E. / Hempelmann, A. / VanStraaten, M.
CitationJournal: Cell Rep / Year: 2021
Title: Nanobody-mediated macromolecular crowding induces membrane fission and remodeling in the African trypanosome.
Authors: Hempelmann, A. / Hartleb, L. / van Straaten, M. / Hashemi, H. / Zeelen, J.P. / Bongers, K. / Papavasiliou, F.N. / Engstler, M. / Stebbins, C.E. / Jones, N.G.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Variant surface glycoprotein MITAT 1.2
B: Variant surface glycoprotein MITAT 1.2
C: Nanobody VSG2(NB14)
D: Nanobody VSG2(NB14)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,53511
Polymers106,4154
Non-polymers2,1207
Water17,565975
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16310 Å2
ΔGint-35 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.542, 95.950, 124.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Antibody / Sugars , 3 types, 6 molecules ABCD

#1: Protein Variant surface glycoprotein MITAT 1.2 / VSG 221


Mass: 38844.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Glycosylated at N289 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Antibody Nanobody VSG2(NB14)


Mass: 14362.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 980 molecules

#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate, 23 % PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→74.24 Å / Num. obs: 266024 / % possible obs: 98.27 % / Redundancy: 12.3 % / CC1/2: 1 / Net I/σ(I): 17.72
Reflection shellResolution: 1.3→1.346 Å / Num. unique obs: 23312 / CC1/2: 0.552

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Coot3.25model building
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG, 5lhr(chainB)

1vsg

5lhr


Resolution: 1.3→74.237 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1723 13427 5.05 %
Rwork0.1512 252469 -
obs0.1522 265896 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.37 Å2 / Biso mean: 25.7876 Å2 / Biso min: 11.23 Å2
Refinement stepCycle: final / Resolution: 1.3→74.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 205 975 8030
Biso mean--33.39 31.37 -
Num. residues----932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.31480.31223950.3079702183
1.3148-1.33030.29413670.2848743887
1.3303-1.34650.3134210.2683767090
1.3465-1.36350.25684380.2462788193
1.3635-1.38150.26224380.2228815496
1.3815-1.40040.23674800.2061840899
1.4004-1.42040.23724400.18998489100
1.4204-1.44160.20024680.16988466100
1.4416-1.46410.20414570.15828495100
1.4641-1.48810.17234930.1438437100
1.4881-1.51380.17634370.13728532100
1.5138-1.54130.17374610.13228525100
1.5413-1.5710.1724460.13158540100
1.571-1.6030.15324550.12498506100
1.603-1.63790.15745020.12498440100
1.6379-1.6760.15674220.12578533100
1.676-1.71790.16064700.12738537100
1.7179-1.76440.15154230.12548544100
1.7644-1.81630.16714180.12648599100
1.8163-1.87490.15484310.12638569100
1.8749-1.9420.16264690.13298548100
1.942-2.01970.15324590.1338552100
2.0197-2.11160.15144620.1348580100
2.1116-2.2230.16314380.13158629100
2.223-2.36230.16174670.12948544100
2.3623-2.54470.15744510.13628637100
2.5447-2.80070.15794500.14668684100
2.8007-3.2060.16954440.15828722100
3.206-4.03920.16774510.15828766100
4.0392-74.2370.18824740.17439023100

+
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