[English] 日本語
Yorodumi
- PDB-6r7t: Crystal Structure of human Melanoma-associated antigen B1 (MAGEB1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r7t
TitleCrystal Structure of human Melanoma-associated antigen B1 (MAGEB1) in complex with nanobody
Components
  • Melanoma-associated antigen B1
  • anti MAGEB1 nanobody
KeywordsIMMUNE SYSTEM / Melanoma
Function / homology
Function and homology information


negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
MAGE homology domain, winged helix WH2 motif / Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain ...MAGE homology domain, winged helix WH2 motif / Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Melanoma-associated antigen B1
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.682 Å
AuthorsYe, M. / Newman, J. / Pike, A.C.W. / Burgess-Brown, N. / Cooper, C.D.O. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Gileadi, O. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of Melanoma-associated antigen B1 (MAGEB1) in complex with nanobody
Authors: Ye, M. / Newman, J. / Pike, A.C.W. / Burgess-Brown, N. / Cooper, C.D.O. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Gileadi, O. / von Delft, F.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / refine / reflns
Item: _refine.pdbx_starting_model / _reflns.pdbx_Rmerge_I_obs
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti MAGEB1 nanobody
B: Melanoma-associated antigen B1


Theoretical massNumber of molelcules
Total (without water)42,3232
Polymers42,3232
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-12 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.976, 61.976, 361.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Antibody anti MAGEB1 nanobody


Mass: 13119.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein Melanoma-associated antigen B1 / Cancer/testis antigen 3.1 / CT3.1 / DSS-AHC critical interval MAGE superfamily 10 / DAM10 / MAGE-B1 ...Cancer/testis antigen 3.1 / CT3.1 / DSS-AHC critical interval MAGE superfamily 10 / DAM10 / MAGE-B1 antigen / MAGE-XP antigen


Mass: 29203.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGEB1, MAGEL1, MAGEXP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P43366
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.056M sodium phosphate monobasic - 1.344M potassium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.68→53.673 Å / Num. obs: 12641 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 12.1
Reflection shellResolution: 2.68→2.81 Å / Num. unique obs: 1618

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WA0

2wa0


Resolution: 2.682→53.673 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.92
RfactorNum. reflection% reflection
Rfree0.2883 625 5 %
Rwork0.2579 --
obs0.2594 12491 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.682→53.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 0 43 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022454
X-RAY DIFFRACTIONf_angle_d0.523312
X-RAY DIFFRACTIONf_dihedral_angle_d17.2471452
X-RAY DIFFRACTIONf_chiral_restr0.037350
X-RAY DIFFRACTIONf_plane_restr0.004423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6815-2.95130.41531500.33532860X-RAY DIFFRACTION100
2.9513-3.37830.40191450.29942872X-RAY DIFFRACTION99
3.3783-4.25610.2961680.23752930X-RAY DIFFRACTION100
4.2561-53.68330.2321620.24463204X-RAY DIFFRACTION99

+
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