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- PDB-6r7t: Crystal Structure of human Melanoma-associated antigen B1 (MAGEB1... -

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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
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.36 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

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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

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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

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