[English] 日本語
Yorodumi
- PDB-5c0n: Development of a monoclonal antibody targeting secreted aP2 to tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c0n
TitleDevelopment of a monoclonal antibody targeting secreted aP2 to treat diabetes and fatty liver disease
Components
  • Fab CA33 Heavy chain
  • Fab CA33 light chain
  • Fatty acid-binding protein, adipocyte
KeywordsLIPID TRANSPORT / AP2 / FABP4 / Fab / type II diabetes
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Immunoglobulins / Beta Barrel ...Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDoyle, C.
CitationJournal: Sci Transl Med / Year: 2015
Title: Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes.
Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / ...Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / West, S. / Garlish, R. / Neale, H. / Doyle, C. / Moore, A. / Hotamisligil, G.S.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
H: Fab CA33 Heavy chain
L: Fab CA33 light chain
B: Fatty acid-binding protein, adipocyte
C: Fab CA33 Heavy chain
D: Fab CA33 light chain


Theoretical massNumber of molelcules
Total (without water)124,1396
Polymers124,1396
Non-polymers00
Water00
1
A: Fatty acid-binding protein, adipocyte
H: Fab CA33 Heavy chain
L: Fab CA33 light chain


Theoretical massNumber of molelcules
Total (without water)62,0703
Polymers62,0703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, adipocyte
C: Fab CA33 Heavy chain
D: Fab CA33 light chain


Theoretical massNumber of molelcules
Total (without water)62,0703
Polymers62,0703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.270, 101.950, 95.320
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12H
22C
13L
23D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSALAALAAA1 - 1312 - 132
21CYSCYSALAALABD1 - 1312 - 132
12GLNGLNVALVALHB1 - 2181 - 218
22GLNGLNVALVALCE1 - 2181 - 218
13ASPASPARGARGLC1 - 2161 - 216
23ASPASPARGARGDF1 - 2161 - 216

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Fatty acid-binding protein, adipocyte / AP2 / 3T3-L1 lipid-binding protein / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty ...AP2 / 3T3-L1 lipid-binding protein / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4 / Myelin P2 protein homolog / P15 / P2 adipocyte protein / Protein 422


Mass: 14670.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4, Ap2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04117
#2: Antibody Fab CA33 Heavy chain


Mass: 23379.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab CA33 light chain


Mass: 24019.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes pH 7.5, 0.2M NH2SO4, 16% PEG 4K and 10% isopropanol

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.95→54.97 Å / Num. obs: 26312 / % possible obs: 99.2 % / Redundancy: 6.16 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.3
Reflection shellResolution: 2.95→3.09 Å / Num. unique all: 3489

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIE

1lie


Resolution: 3→54.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.884 / SU B: 21.712 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26464 2466 9.9 %RANDOM
Rwork0.18636 ---
obs0.19425 22426 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-5.01 Å2
2---3.51 Å2-0 Å2
3---3.77 Å2
Refinement stepCycle: 1 / Resolution: 3→54.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8541 0 0 0 8541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.028740
X-RAY DIFFRACTIONr_bond_other_d0.0040.028054
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.95411901
X-RAY DIFFRACTIONr_angle_other_deg1.085318667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3151116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52524.118323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.143151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1351536
X-RAY DIFFRACTIONr_chiral_restr0.0850.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219789
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021883
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_it4.8435.9764488
X-RAY DIFFRACTIONr_mcbond_other4.8425.9774487
X-RAY DIFFRACTIONr_mcangle_it7.6448.9565596
X-RAY DIFFRACTIONr_mcangle_other7.6438.9565597
X-RAY DIFFRACTIONr_scbond_it4.6636.2684252
X-RAY DIFFRACTIONr_scbond_other4.6636.2694253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.339.2256306
X-RAY DIFFRACTIONr_long_range_B_refined10.83247.1689257
X-RAY DIFFRACTIONr_long_range_B_other10.83247.1719258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72800.12
12B72800.12
21H107110.12
22C107110.12
31L107540.14
32D107540.14
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 189 -
Rwork0.282 1679 -
obs--98.16 %

+
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