[English] 日本語
Yorodumi
- PDB-7p57: VSG2 mutant structure lacking the calcium binding pocket -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p57
TitleVSG2 mutant structure lacking the calcium binding pocket
ComponentsVariant surface glycoprotein MITAT 1.2
KeywordsMEMBRANE PROTEIN / Variant Surface Glycoprotein / Coat / Trypanosoma brucei / African trypanosome / Immune Evasion / antigenic variation / calcium binding / calcium
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / symbiont-mediated evasion of host immune response / side of membrane / plasma membrane / Variant surface glycoprotein MITAT 1.2
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 Å
AuthorsGkeka, A. / Aresta-Branco, F. / Stebbins, C.E. / Papavasiliou, F.N.
Citation
Journal: Cell Rep / Year: 2023
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome.
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, ...Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, C.E. / Papavasiliou, F.N.
#1: Journal: Biorxiv / Year: 2022
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Stebbins, C.E. / Papavasiliou, F.N.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7202
Polymers50,9711
Non-polymers7491
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, The biological assembly is a dimer., isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint20 kcal/mol
Surface area17980 Å2
MethodPISA
2
A: Variant surface glycoprotein MITAT 1.2
hetero molecules

A: Variant surface glycoprotein MITAT 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4404
Polymers101,9432
Non-polymers1,4972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area11480 Å2
ΔGint-7 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.015, 96.015, 108.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

-
Components

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


Mass: 50971.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VSG2 "AAA mutant" (D208, N209, and D210 each mutated to alanine).
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Cell line (production host): FAB 3.6.4 (VSG2-AAA) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: 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.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 39% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.961→48.01 Å / Num. obs: 36675 / % possible obs: 99.24 % / Redundancy: 19.7 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09816 / Rpim(I) all: 0.02123 / Rrim(I) all: 0.1006 / Net I/σ(I): 20.27
Reflection shellResolution: 1.961→2.031 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8934 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 3341 / CC1/2: 0.557 / CC star: 0.846 / Rpim(I) all: 0.4747 / Rrim(I) all: 1.023 / % possible all: 92.39

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG

1vsg


Resolution: 1.961→48.01 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 3400 5 %
Rwork0.1603 64591 -
obs0.162 36675 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.86 Å2 / Biso mean: 43.8988 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 1.961→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 50 239 2953
Biso mean--58.31 46.03 -
Num. residues----359
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.961-1.98910.3479940.3575179866
1.9891-2.01880.35631300.313245590
2.0188-2.05030.28791390.2778267697
2.0503-2.08390.29461440.2655275399
2.0839-2.11980.28021490.22322735100
2.1198-2.15840.24411420.20352720100
2.1584-2.19990.21591450.18072741100
2.1999-2.24480.18831420.16672768100
2.2448-2.29360.20321460.17022748100
2.2936-2.3470.17611440.15662753100
2.347-2.40570.21511490.14562754100
2.4057-2.47070.1681450.15282709100
2.4707-2.54340.18461450.15022733100
2.5434-2.62550.18221460.14582771100
2.6255-2.71930.20221440.14372747100
2.7193-2.82820.17031450.15372770100
2.8282-2.95690.23871410.16612726100
2.9569-3.11280.21151410.17572757100
3.1128-3.30770.25151470.17952745100
3.3077-3.56310.19031470.16742728100
3.5631-3.92150.16831470.14492746100
3.9215-4.48860.16131390.12292756100
4.4886-5.65370.14721450.14042763100
5.6537-48.010.17231440.14332739100
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)
12.9789-3.2781-0.51066.85851.19160.74730.15650.3118-0.3089-0.1233-0.0977-0.25970.13320.081-0.0610.2981-0.0169-0.05370.3131-0.0780.299-2.3456-10.686420.1191
27.4673-5.31722.27214.7829-1.91981.412-0.0899-0.2151-0.26210.09760.18460.3291-0.0348-0.243-0.10730.2436-0.0370.00260.23910.01650.2066-30.802120.999724.919
32.5478-1.2387-0.66233.01940.98311.53570.11860.3325-0.3379-0.16290.037-0.36620.18470.1304-0.13930.30130.0023-0.04970.3133-0.09620.33294.9795-11.564419.1615
43.23180.41453.26928.8586-3.33085.85950.05710.30720.0833-0.3588-0.08580.464-0.2002-0.1802-0.09870.31740.0126-0.02680.3173-0.04430.3371-11.7525-6.187218.9748
52.9947-1.21330.37862.1250.18281.09350.13010.1634-1.02320.2440.0931-0.36840.4340.1986-0.20970.50410.0625-0.15430.2914-0.0440.63538.4195-25.168828.9931
66.66261.99624.50192.2531.95183.25490.3007-1.139-0.21140.9749-0.1680.05970.2743-0.3642-0.13560.4422-0.0464-0.01950.36570.00970.2843-5.7779-12.838535.6786
71.97821.73620.09692.00790.39950.1867-0.0294-0.1305-0.0961-0.27390.18930.6616-0.0664-0.0375-0.16780.2761-0.0221-0.01390.32850.00290.3252-18.77560.488628.5411
88.0523-3.6975-4.1987.98663.04464.6016-0.4733-0.9189-0.73270.98150.40660.73980.44620.22570.1840.33390.02010.0130.43910.18990.4396-39.827216.469134.207
95.35891.7704-1.56524.5449-1.72534.7744-0.07920.1895-0.2762-0.22690.18630.43870.2504-0.4642-0.09960.2390.0387-0.06580.24880.02790.3148-37.068922.836218.7155
103.7407-2.1481-5.40617.6686.69119.76750.54140.08530.4184-0.4613-0.3220.3977-1.2497-0.4267-0.36080.51960.05650.02570.37810.07490.3981-34.673741.591223.6614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:62)A27 - 62
2X-RAY DIFFRACTION2(chain A and resid 63:111)A63 - 111
3X-RAY DIFFRACTION3(chain A and resid 112:178)A112 - 178
4X-RAY DIFFRACTION4(chain A and resid 179:190)A179 - 190
5X-RAY DIFFRACTION5(chain A and resid 191:256)A191 - 256
6X-RAY DIFFRACTION6(chain A and resid 257:273)A257 - 273
7X-RAY DIFFRACTION7(chain A and resid 274:287)A274 - 287
8X-RAY DIFFRACTION8(chain A and resid 288:313)A288 - 313
9X-RAY DIFFRACTION9(chain A and resid 314:375)A314 - 375
10X-RAY DIFFRACTION10(chain A and resid 376:385)A376 - 385

+
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