[English] 日本語
Yorodumi
- PDB-5dvm: Fc Design 20.8.37 B chain homodimer E357D/S364R/Y407A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dvm
TitleFc Design 20.8.37 B chain homodimer E357D/S364R/Y407A
Components
  • Fc-III peptide
  • Ig gamma-1 chain C region
KeywordsIMMUNE SYSTEM / head-to-tail homodimer / Immunoglobulin / Fc
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å
Model detailsDesign XXX
AuthorsAtwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. ...Atwell, S. / Leaver-Fay, A. / Froning, K.J. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Dhanani, S.H. / Chamberlain, A.K. / Fitchett, J.R. / Gutierrez, B. / Hendle, J. / Demarest, S.J. / Kuhlman, B.
CitationJournal: Structure / Year: 2016
Title: Computationally Designed Bispecific Antibodies using Negative State Repertoires.
Authors: Leaver-Fay, A. / Froning, K.J. / Atwell, S. / Aldaz, H. / Pustilnik, A. / Lu, F. / Huang, F. / Yuan, R. / Hassanali, S. / Chamberlain, A.K. / Fitchett, J.R. / Demarest, S.J. / Kuhlman, B.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Data collection
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)27,1112
Polymers27,1112
Non-polymers00
Water1267
1
A: Ig gamma-1 chain C region
B: Fc-III peptide

A: Ig gamma-1 chain C region
B: Fc-III peptide


Theoretical massNumber of molelcules
Total (without water)54,2224
Polymers54,2224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5250 Å2
ΔGint-39 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.197, 107.197, 56.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Ig gamma-1 chain C region


Mass: 25577.012 Da / Num. of mol.: 1 / Fragment: UNP residues 104-330 / Mutation: E357D, S364R, Y407A
Source method: isolated from a genetically manipulated source
Details: transient expression / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Protein/peptide Fc-III peptide


Mass: 1533.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.76 Å3/Da / Density % sol: 67.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: 100mM Sodium Cacodylate pH 6.5 + 20% PEG 8K + 200mM Magnesium Acetate tetrahydrate

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2014 / Details: Diamond (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 8056 / % possible obs: 98.7 % / Redundancy: 5.7 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Rsym value: 0.136 / Net I/av σ(I): 4.279 / Net I/σ(I): 7.9 / Num. measured all: 45883
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.95-3.1130.7961323510840.6310.7961.192.3
3.11-3.33.90.5091.5431210930.3280.5092.199.1
3.3-3.535.90.2922.5618210430.1350.2924.6100
3.53-3.816.80.2233.267449880.0920.2236.4100
3.81-4.176.80.1474.660028870.060.1479.4100
4.17-4.676.80.1115.356348340.0450.11112.399.9
4.67-5.396.70.115.447897190.0440.1113.6100
5.39-6.66.60.1085.441296230.0450.10813.5100
6.6-9.336.50.096.132214990.0370.0915.999.9
9.33-92.8355.70.0836.416352860.0370.08316.599.1

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0017refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
XDSdata reduction
RefinementResolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.583 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.948 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 370 4.6 %RANDOM
Rwork0.223 ---
obs0.2261 7658 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.5 Å2 / Biso mean: 69.424 Å2 / Biso min: 32.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å21.27 Å20 Å2
2--2.54 Å20 Å2
3----3.81 Å2
Refinement stepCycle: final / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 0 7 1701
Biso mean---51.33 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021746
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.9462396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.865218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59124.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66515257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.906156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221337
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 32 -
Rwork0.326 474 -
all-506 -
obs--86.79 %

+
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