[English] 日本語
Yorodumi
- PDB-6hyg: Heteromeric tandem IgG4/IgG1 Fc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hyg
TitleHeteromeric tandem IgG4/IgG1 Fc
ComponentsIgHG1 and IgHG4 hybrid
KeywordsIMMUNE SYSTEM / immunoglobulin / Fc
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsCasaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. ...Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM.
Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. ...Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
History
DepositionOct 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 16, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IgHG1 and IgHG4 hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6483
Polymers53,5181
Non-polymers1312
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-47 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.119, 63.253, 77.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein IgHG1 and IgHG4 hybrid


Mass: 53517.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-K1-GS / Production host: Cricetulus griseus (Chinese hamster)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 mM zinc acetate, 100 mM sodium cacodylate pH 6.5, 9 % (w/v) polyethylene glycol 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.507
11h,-k,-l20.493
ReflectionResolution: 2.31→29.28 Å / Num. obs: 27962 / % possible obs: 95.7 % / Redundancy: 3.1 % / Net I/σ(I): 8.4
Reflection shellResolution: 2.31→2.39 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2S

3c2s


Resolution: 2.31→29.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.671 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27719 1353 4.8 %RANDOM
Rwork0.25759 ---
obs0.25858 26607 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.441 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.89 Å2
2--5.78 Å20 Å2
3----5.08 Å2
Refinement stepCycle: 1 / Resolution: 2.31→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 2 92 3419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133418
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173070
X-RAY DIFFRACTIONr_angle_refined_deg2.3981.6494651
X-RAY DIFFRACTIONr_angle_other_deg1.5241.5747209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.695414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67724.132167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33215587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9521512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023756
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2622.6371662
X-RAY DIFFRACTIONr_mcbond_other2.2612.6361661
X-RAY DIFFRACTIONr_mcangle_it3.5073.9452074
X-RAY DIFFRACTIONr_mcangle_other3.5063.9462075
X-RAY DIFFRACTIONr_scbond_it2.5212.8571756
X-RAY DIFFRACTIONr_scbond_other2.5212.8571756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8224.1742578
X-RAY DIFFRACTIONr_long_range_B_refined5.94629.7823604
X-RAY DIFFRACTIONr_long_range_B_other5.9329.6453583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.307→2.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.923 99 -
Rwork0.896 1921 -
obs--94.26 %
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)
12.590.03460.35011.8358-0.08211.4463-0.1551-0.0940.05590.2859-0.0333-0.319-0.04910.11930.18830.17970.007-0.05680.12170.04070.081125.366-30.97132.75
22.6567-0.0719-0.30921.7812-0.03721.5006-0.1270.1168-0.055-0.2626-0.0451-0.31710.02550.11410.1720.1875-0.00970.04440.10640.04050.080525.275-33.7436.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 224
2X-RAY DIFFRACTION2A282 - 489

+
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