[English] 日本語
Yorodumi
- PDB-5b71: Crystal structure of complement C5 in complex with SKY59 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b71
TitleCrystal structure of complement C5 in complex with SKY59
Components
  • Complement C5 beta chain
  • SKY59 Fab heavy chain
  • SKY59 Fab light chain
KeywordsIMMUNE SYSTEM / pH-dependent / recycling antibody / complement C5 / Fab / Complex
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Macroglobulin (MG2) domain / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain ...Macroglobulin (MG2) domain / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsIrie, M. / Shimizu, Y. / Sampei, Z. / Fukuzawa, T.
CitationJournal: Sci Rep / Year: 2017
Title: Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases.
Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / ...Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / Iwayanagi, Y. / Shibahara, N. / Shibuya, M. / Nakamura, G. / Nambu, T. / Hayasaka, A. / Mimoto, F. / Okura, Y. / Hori, Y. / Habu, K. / Wada, M. / Miura, T. / Tachibana, T. / Honda, K. / Tsunoda, H. / Kitazawa, T. / Kawabe, Y. / Igawa, T. / Hattori, K. / Nezu, J.
History
DepositionJun 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SKY59 Fab light chain
B: SKY59 Fab heavy chain
C: SKY59 Fab light chain
D: SKY59 Fab heavy chain
E: Complement C5 beta chain
F: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)119,4956
Polymers119,4956
Non-polymers00
Water5,801322
1
A: SKY59 Fab light chain
B: SKY59 Fab heavy chain
E: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)59,7483
Polymers59,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-28 kcal/mol
Surface area23950 Å2
MethodPISA
2
C: SKY59 Fab light chain
D: SKY59 Fab heavy chain
F: Complement C5 beta chain


Theoretical massNumber of molelcules
Total (without water)59,7483
Polymers59,7483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-31 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.790, 55.100, 127.760
Angle α, β, γ (deg.)89.180, 86.240, 78.200
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody SKY59 Fab light chain


Mass: 23328.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody SKY59 Fab heavy chain


Mass: 24121.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein Complement C5 beta chain


Mass: 12297.792 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01031
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium formate dehydrate, 15.0% w/v polyethylene glycol 3350, 20% v/v glycerol as cryoprotectant

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→42.49 Å / Num. obs: 56154 / % possible obs: 92.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.9
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.8 / % possible all: 95.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata processing
Aimlessdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBJ, 3CU7

1bbj

3cu7


Resolution: 2.11→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.455 / SU ML: 0.233 / SU R Cruickshank DPI: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 2724 4.9 %RANDOM
Rwork0.2459 ---
obs0.2478 53398 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 38.604 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20.86 Å21.39 Å2
2---0.39 Å21.52 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 2.11→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 0 322 8217
Biso mean---39.29 -
Num. residues----1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198085
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.94211004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.82751047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22924.161298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5721524
X-RAY DIFFRACTIONr_chiral_restr0.060.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216030
X-RAY DIFFRACTIONr_mcbond_it0.7173.9344218
X-RAY DIFFRACTIONr_mcangle_it1.3325.8925255
X-RAY DIFFRACTIONr_scbond_it0.463.8983867
LS refinement shellResolution: 2.11→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 210 -
Rwork0.357 4034 -
all-4244 -
obs--95.74 %

+
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