[English] 日本語
Yorodumi
- PDB-6pyc: Structure of kappa-on-heavy (KoH) antibody Fab bound to the cardi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pyc
TitleStructure of kappa-on-heavy (KoH) antibody Fab bound to the cardiac hormone marinobufagenin
Components
  • (KoH body Fab ...) x 2
  • (anti-kappa antibody Fab ...) x 2
KeywordsIMMUNE SYSTEM / Marinobufagenin / antibody engineering / Bence-Jones dimer
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-P4S
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFranklin, M.C. / Macdonald, L.E. / McWhirter, J. / Murphy, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Kappa-on-Heavy (KoH) bodies are a distinct class of fully-human antibody-like therapeutic agents with antigen-binding properties.
Authors: Macdonald, L.E. / Meagher, K.A. / Franklin, M.C. / Levenkova, N. / Hansen, J. / Badithe, A.T. / Zhong, M. / Krueger, P. / Rafique, A. / Tu, N. / Shevchuk, J. / Wadhwa, S. / Ehrlich, G. / ...Authors: Macdonald, L.E. / Meagher, K.A. / Franklin, M.C. / Levenkova, N. / Hansen, J. / Badithe, A.T. / Zhong, M. / Krueger, P. / Rafique, A. / Tu, N. / Shevchuk, J. / Wadhwa, S. / Ehrlich, G. / Bautista, J. / Grant, C. / Esau, L. / Poueymirou, W.T. / Auerbach, W. / Morton, L. / Babb, R. / Chen, G. / Huang, T. / MacDonald, D. / Graham, K. / Gurer, C. / Voronina, V.A. / McWhirter, J.R. / Guo, C. / Yancopoulos, G.D. / Murphy, A.J.
History
DepositionJul 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: 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 1.4Oct 16, 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
H: KoH body Fab heavy chain
L: KoH body Fab light chain
A: anti-kappa antibody Fab heavy chain
B: anti-kappa antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4067
Polymers94,5094
Non-polymers8973
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, Anti-kappa antibody is a crystallization aid, not required for the KoH Fab binding to marinobufagenin.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.483, 128.483, 333.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

-
Antibody , 4 types, 4 molecules HLAB

#1: Antibody KoH body Fab heavy chain


Mass: 23150.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody KoH body Fab light chain


Mass: 23586.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody anti-kappa antibody Fab heavy chain


Mass: 23943.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody anti-kappa antibody Fab light chain


Mass: 23828.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

-
Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-P4S / (3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide


Mass: 400.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H32O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid; 0.8 M ammonium sulfate; pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.6→100 Å / Num. obs: 15341 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.111 / Rrim(I) all: 0.32 / Net I/σ(I): 5.5
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.118 / Num. unique obs: 766 / CC1/2: 0.539 / Rpim(I) all: 0.452 / Rrim(I) all: 1.215 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YHY, 5DQD, 4LRN, 1EEQ, 4WCY

4yhy

5dqd

4lrn

1eeq

4wcy


Resolution: 3.6→47.44 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.837 / WRfactor Rfree: 0.2691 / WRfactor Rwork: 0.2232 / FOM work R set: 0.7847 / SU B: 84.457 / SU ML: 0.565 / SU R Cruickshank DPI: 0.607 / SU Rfree: 0.7491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.749 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 711 4.8 %RANDOM
Rwork0.2339 ---
obs0.2364 14000 88.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 226.81 Å2 / Biso mean: 92.198 Å2 / Biso min: 47.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---1.63 Å20 Å2
3---3.26 Å2
Refinement stepCycle: final / Resolution: 3.6→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 63 0 6538
Biso mean--73.18 --
Num. residues----843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136712
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176015
X-RAY DIFFRACTIONr_angle_refined_deg1.391.6639163
X-RAY DIFFRACTIONr_angle_other_deg1.2151.58514055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6715837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0122.852291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.483151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7071528
X-RAY DIFFRACTIONr_chiral_restr0.060.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_mcbond_it0.6054.6063366
X-RAY DIFFRACTIONr_mcbond_other0.6054.6063365
X-RAY DIFFRACTIONr_mcangle_it1.096.9094197
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 47 -
Rwork0.343 882 -
all-929 -
obs--77.03 %
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)
14.80713.21950.81594.98810.00665.23040.6044-0.6923-0.59581.0401-0.3956-0.3880.22120.0511-0.20890.4003-0.0691-0.07280.11870.01880.456928.421112.36572.395
23.7490.5722-0.55695.4914-1.26589.8783-0.1375-0.05670.25170.41470.1172-0.1551-0.1706-0.05370.02030.09750.1292-0.11530.2921-0.11470.306646.096143.60272.533
31.48181.5968-0.225310.94010.99364.7835-0.02330.28540.1407-0.25770.17870.3252-0.07440.0614-0.15540.01190.0097-0.03760.12450.00440.328222.947121.64152.428
48.007-0.71024.11751.0928-0.19746.0190.08150.3255-0.10660.060.0637-0.3870.37750.5899-0.14520.12490.08290.05470.1084-0.04010.405852.708139.11757.541
54.03550.5673-1.03564.13520.46886.2780.2350.54580.4954-0.3604-0.1528-0.478-0.47990.7328-0.08220.26110.0196-0.05060.34760.15990.572942.862159.50137
65.50593.44023.38582.23991.91492.902-0.0626-0.21.09490.1961-0.23450.6594-1.1022-0.28610.2971.67540.24220.09471.02660.41351.464628.307177.94516.487
76.164-0.62210.99224.8384-1.19937.22730.24140.7203-0.5376-0.85910.03160.1030.2851-0.3401-0.2730.35890.05270.00880.3875-0.07050.196628.244144.55227.486
83.98691.85830.46121.71462.01763.9126-0.52181.09360.8915-0.80440.50230.3979-1.1660.26970.01951.41770.5001-0.0261.67890.50630.715527.118171.5631.196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 112
2X-RAY DIFFRACTION2H113 - 212
3X-RAY DIFFRACTION3L1 - 107
4X-RAY DIFFRACTION4L108 - 213
5X-RAY DIFFRACTION5A1 - 118
6X-RAY DIFFRACTION6A119 - 218
7X-RAY DIFFRACTION7B1 - 107
8X-RAY DIFFRACTION8B108 - 213

+
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