[English] 日本語
Yorodumi
- PDB-7uen: Genetic and structural basis of the human anti-alpha-galactosyl a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uen
TitleGenetic and structural basis of the human anti-alpha-galactosyl antibody response
Components(M86 antibody Fab ...) x 2
KeywordsIMMUNE SYSTEM / alpha-galactosyl / antibody / anti-alpha-gal / immune response / M86
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Genetic and structural basis of the human anti-alpha-galactosyl antibody response.
Authors: Langley, D.B. / Schofield, P. / Nevoltris, D. / Jackson, J. / Jackson, K.J.L. / Peters, T.J. / Burk, M. / Matthews, J.M. / Basten, A. / Goodnow, C.C. / van Nunen, S. / Reed, J.H. / Christ, D.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 29, 2022ID: 6NUY
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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
L: M86 antibody Fab light chain
H: M86 antibody Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6485
Polymers49,1722
Non-polymers4763
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The two chains hold together over gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-23 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.492, 101.492, 78.159
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-444-

HOH

21L-457-

HOH

31L-604-

HOH

41H-459-

HOH

-
Components

-
Antibody , 2 types, 2 molecules LH

#1: Antibody M86 antibody Fab light chain


Mass: 24065.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody M86 antibody Fab heavy chain


Mass: 25106.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 349 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Equal volumes of a protein (in 25 mM Tris (pH 8.0), 100 mM NaCl) and well solution (1.5 M NaH2PO4.H2O.K2HPO4, pH 8.0) were combined.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→38.31 Å / Num. obs: 67630 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.093 / Net I/σ(I): 17.2 / Num. measured all: 1276211 / Scaling rejects: 224
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
1.55-1.5814.31.7574750833190.4650.4751.8222.599.9
8.49-38.3115.90.05774194670.9980.0150.05945.499.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.91 Å42.63 Å
Translation5.91 Å42.63 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 1.55→38.31 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.111 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 3288 4.9 %RANDOM
Rwork0.1276 ---
obs0.1298 64307 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 27.962 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.55→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 45 347 3588
Biso mean--24.81 39.79 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143128
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6444845
X-RAY DIFFRACTIONr_angle_other_deg1.4521.5827248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12922.887142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3511512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024548
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02800
X-RAY DIFFRACTIONr_rigid_bond_restr3.29636654
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 253 -
Rwork0.246 4694 -
all-4947 -
obs--99.82 %

+
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