[English] 日本語
Yorodumi
- PDB-6z7w: Human insulin in complex with the analytical antibody HUI-018 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z7w
TitleHuman insulin in complex with the analytical antibody HUI-018 Fab
Components
  • (Insulin) x 2
  • HUI-018 Fab Heavy Chain
  • MAb 6H10 light chain
KeywordsHORMONE / complex / insulin / analytical antibody / Fab
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsJohansson, E.
CitationJournal: Protein Sci. / Year: 2021
Title: Insulin binding to the analytical antibody sandwich pair OXI-005 and HUI-018: Epitope mapping and binding properties.
Authors: Johansson, E. / Wu, X. / Yu, B. / Yang, Z. / Cao, Z. / Wiberg, C. / Jeppesen, C.B. / Poulsen, F.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin
K: Insulin
L: Insulin
M: Insulin
N: Insulin
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)213,39416
Polymers213,39416
Non-polymers00
Water12,845713
1
A: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MAb 6H10 light chain
B: HUI-018 Fab Heavy Chain
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
I: Insulin
J: Insulin
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)106,6978
Polymers106,6978
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
K: Insulin
L: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: MAb 6H10 light chain
D: HUI-018 Fab Heavy Chain
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
K: Insulin
L: Insulin
M: Insulin
N: Insulin


Theoretical massNumber of molelcules
Total (without water)106,6978
Polymers106,6978
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MAb 6H10 light chain
F: HUI-018 Fab Heavy Chain
M: Insulin
N: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: MAb 6H10 light chain
H: HUI-018 Fab Heavy Chain
O: Insulin
P: Insulin


Theoretical massNumber of molelcules
Total (without water)53,3494
Polymers53,3494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.230, 216.610, 101.090
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 213)
d_2ens_1chain "C"
d_3ens_1(chain "E" and resid 1 through 213)
d_4ens_1(chain "G" and resid 1 through 213)
d_1ens_2(chain "B" and (resid 1 through 130 or resid 138 through 216))
d_2ens_2chain "D"
d_3ens_2(chain "F" and resid 1 through 216)
d_4ens_2(chain "H" and (resid 1 through 130 or resid 138 through 216))
d_1ens_3chain "J"
d_2ens_3chain "L"
d_3ens_3(chain "N" and resid 5 through 28)
d_4ens_3(chain "P" and resid 5 through 28)
d_1ens_4chain "K"
d_2ens_4chain "M"
d_3ens_4chain "O"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLUA1 - 213
d_21ens_1ASPGLUC1 - 213
d_31ens_1ASPGLUE1 - 213
d_41ens_1ASPGLUG1 - 213
d_11ens_2GLNPROB1 - 134
d_12ens_2SERPROB138 - 216
d_21ens_2GLNPROD1 - 213
d_31ens_2GLNPROF1 - 213
d_41ens_2GLNPROH1 - 134
d_42ens_2SERPROH138 - 216
d_11ens_3HISPROJ1 - 24
d_21ens_3HISPROL1 - 24
d_31ens_3HISPRON1 - 24
d_41ens_3HISPROP2 - 25
d_11ens_4GLYASNK1 - 21
d_21ens_4GLYASNM1 - 21
d_31ens_4GLYASNO1 - 21

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

-
Components

#1: Antibody
MAb 6H10 light chain


Mass: 23809.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Production host: Homo sapiens (human)
#2: Antibody
HUI-018 Fab Heavy Chain


Mass: 23721.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide
Insulin /


Mass: 2383.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#4: Protein/peptide
Insulin /


Mass: 3433.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Hepes, pH 7, 20 % (v/w) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→29.9 Å / Num. obs: 77030 / % possible obs: 96.78 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.51 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.07496 / Rrim(I) all: 0.1313 / Net I/σ(I): 9.06
Reflection shellResolution: 2.42→2.597 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.7945 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 17424 / CC1/2: 0.565 / CC star: 0.85 / Rpim(I) all: 0.6057 / Rrim(I) all: 1.004 / % possible all: 90.97

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1200000000 / Resolution: 2.42→29.87 Å / SU ML: 0.4385 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 31.9015
RfactorNum. reflection% reflection
Rfree0.2746 3581 2.53 %
Rwork0.2093 --
obs0.2109 77014 89.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.78 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14579 0 0 713 15292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009814911
X-RAY DIFFRACTIONf_angle_d1.346620300
X-RAY DIFFRACTIONf_chiral_restr0.06582315
X-RAY DIFFRACTIONf_plane_restr0.00912590
X-RAY DIFFRACTIONf_dihedral_angle_d20.22395299
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.78453811597
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.95904421613
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.778384878914
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.876134102385
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.0809613821
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.856144309232
ens_3d_2JX-RAY DIFFRACTIONTorsion NCS1.63170219855
ens_3d_3JX-RAY DIFFRACTIONTorsion NCS1.47540600251
ens_3d_4JX-RAY DIFFRACTIONTorsion NCS1.66656843668
ens_4d_2KX-RAY DIFFRACTIONTorsion NCS1.06282542696
ens_4d_3KX-RAY DIFFRACTIONTorsion NCS1.15016509493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.450.41000.36033870X-RAY DIFFRACTION66.94
2.45-2.480.41771220.35125228X-RAY DIFFRACTION86.89
2.48-2.520.42781420.32855293X-RAY DIFFRACTION87.89
2.52-2.560.4021320.31685168X-RAY DIFFRACTION89.36
2.56-2.60.37941480.32065374X-RAY DIFFRACTION89.7
2.6-2.640.35271340.30345387X-RAY DIFFRACTION90.17
2.64-2.680.36911400.29925295X-RAY DIFFRACTION90.03
2.68-2.730.34821300.29095317X-RAY DIFFRACTION89.84
2.73-2.790.34751390.27735465X-RAY DIFFRACTION91.46
2.79-2.840.35591420.28485324X-RAY DIFFRACTION91.33
2.84-2.90.42991540.27125394X-RAY DIFFRACTION91.04
2.9-2.970.37461510.25075491X-RAY DIFFRACTION92.16
2.97-3.050.27511370.23715314X-RAY DIFFRACTION90.97
3.05-3.130.27881400.22315565X-RAY DIFFRACTION92.55
3.13-3.220.31581440.21425382X-RAY DIFFRACTION91.84
3.22-3.320.27561430.21585508X-RAY DIFFRACTION91.78
3.32-3.440.30341350.2035424X-RAY DIFFRACTION92.42
3.44-3.580.27661530.18945484X-RAY DIFFRACTION91.7
3.58-3.740.22811350.185414X-RAY DIFFRACTION92.01
3.74-3.940.26431370.17145428X-RAY DIFFRACTION91.86
3.94-4.190.22761370.15955487X-RAY DIFFRACTION91.45
4.19-4.510.17391300.14255294X-RAY DIFFRACTION90.04
4.51-4.960.2011390.14245336X-RAY DIFFRACTION89.7
4.96-5.670.20781460.15815377X-RAY DIFFRACTION90.79
5.67-7.130.24641430.1895346X-RAY DIFFRACTION90.49
7.13-29.870.18181280.17425275X-RAY DIFFRACTION89

+
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