[English] 日本語
Yorodumi
- PDB-9puo: Neutralizing monoclonal antibody Fab fragment bound to leptin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9puo
TitleNeutralizing monoclonal antibody Fab fragment bound to leptin
Components
  • Leptin
  • Neutralizing antibody Fab fragment, heavy chain
  • Neutralizing antibody Fab fragment, light chain
KeywordsIMMUNE SYSTEM / Antibody / FAB / leptin
Function / homology
Function and homology information


regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / regulation of natural killer cell mediated cytotoxicity / leptin receptor binding ...regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / regulation of natural killer cell mediated cytotoxicity / leptin receptor binding / regulation of bone remodeling / positive regulation of luteinizing hormone secretion / bone growth / regulation of natural killer cell activation / glycerol biosynthetic process / regulation of steroid biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of follicle-stimulating hormone secretion / positive regulation of monoatomic ion transport / regulation of intestinal cholesterol absorption / positive regulation of hepatic stellate cell activation / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / regulation of nitric-oxide synthase activity / adult feeding behavior / activation of protein kinase C activity / bone mineralization involved in bone maturation / sexual reproduction / negative regulation of cartilage development / ovulation from ovarian follicle / negative regulation of D-glucose import / negative regulation of appetite / positive regulation of developmental growth / energy reserve metabolic process / leukocyte tethering or rolling / bile acid metabolic process / cellular response to leptin stimulus / prostaglandin secretion / cardiac muscle hypertrophy / Signaling by Leptin / positive regulation of p38MAPK cascade / hormone metabolic process / cell surface receptor signaling pathway via STAT / intestinal absorption / eating behavior / insulin secretion / aorta development / regulation of gluconeogenesis / negative regulation of vasoconstriction / response to vitamin E / peptide hormone receptor binding / fatty acid beta-oxidation / regulation of cytokine production involved in inflammatory response / central nervous system neuron development / response to dietary excess / T cell differentiation / negative regulation of lipid storage / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of TOR signaling / regulation of angiogenesis / cell surface receptor signaling pathway via JAK-STAT / positive regulation of insulin receptor signaling pathway / adipose tissue development / phagocytosis / cholesterol metabolic process / energy homeostasis / cellular response to retinoic acid / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / regulation of insulin secretion / negative regulation of autophagy / placenta development / response to activity / determination of adult lifespan / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / female pregnancy / response to insulin / circadian rhythm / hormone activity / Transcriptional regulation of white adipocyte differentiation / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / lipid metabolic process / regulation of blood pressure / glucose metabolic process / cellular response to insulin stimulus / positive regulation of reactive oxygen species metabolic process / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / positive regulation of tumor necrosis factor production / response to estradiol / glucose homeostasis / positive regulation of cold-induced thermogenesis / response to ethanol / angiogenesis / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell cycle / positive regulation of MAPK cascade
Similarity search - Function
Leptin / Leptin / Four-helical cytokine-like, core
Similarity search - Domain/homology
PHOSPHATE ION / Leptin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTomchick, D.R. / Wynn, R.M. / Scherer, P.E.
Funding support United States, 12items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK55758 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK099110 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK118620 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK127274 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK131537 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG051459 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK138935 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG084646 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220032 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP150551 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP190561 United States
Robert A. Welch FoundationAU-0042-20030616 United States
CitationJournal: Sci Adv / Year: 2025
Title: Leptin as a key driver for organ fibrogenesis.
Authors: Sun, X.N. / Chen, S. / Zhao, S. / Funcke, J.B. / Virostek, M. / Pedersen, L. / Li, C. / Joung, C. / Lin, Q. / Li, Y. / Cobb, A. / Wang, M.Y. / Min, K. / Maya-Ramos, L. / Degasperi, G. / Liu, ...Authors: Sun, X.N. / Chen, S. / Zhao, S. / Funcke, J.B. / Virostek, M. / Pedersen, L. / Li, C. / Joung, C. / Lin, Q. / Li, Y. / Cobb, A. / Wang, M.Y. / Min, K. / Maya-Ramos, L. / Degasperi, G. / Liu, J. / Zhang, N. / An, Z. / Tomchick, D.R. / Wynn, R.M. / Oh, D.Y. / Scherer, P.E.
History
DepositionJul 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutralizing antibody Fab fragment, heavy chain
B: Neutralizing antibody Fab fragment, light chain
C: Leptin
D: Neutralizing antibody Fab fragment, heavy chain
E: Neutralizing antibody Fab fragment, light chain
F: Leptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3888
Polymers125,1986
Non-polymers1902
Water00
1
A: Neutralizing antibody Fab fragment, heavy chain
B: Neutralizing antibody Fab fragment, light chain
C: Leptin


Theoretical massNumber of molelcules
Total (without water)62,5993
Polymers62,5993
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Neutralizing antibody Fab fragment, heavy chain
E: Neutralizing antibody Fab fragment, light chain
F: Leptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7895
Polymers62,5993
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.927, 48.534, 124.963
Angle α, β, γ (deg.)90.344, 85.206, 70.418
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 25 or resid 29 through 222))
d_2ens_1(chain "D" and (resid 2 through 135 or resid 143 through 222))
d_1ens_2(chain "B" and (resid 1 through 111 or resid 118 through 213))
d_2ens_2(chain "E" and (resid 1 through 57 or resid 60 through 111 or resid 118 through 213))
d_1ens_3(chain "C" and (resid 1 through 25 or resid 49 through 106 or resid 118 through 146))
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALSERSERAA2 - 252 - 25
d_12ens_1PHEPHEPROPROAA29 - 22229 - 222
d_21ens_1VALVALPROPRODD2 - 1352 - 135
d_22ens_1GLYGLYPROPRODD143 - 222143 - 222
d_11ens_2GLNGLNLEULEUBB1 - 1111 - 111
d_12ens_2PROPROPROPROBB118 - 213118 - 213
d_21ens_2GLNGLNPROPROEE1 - 571 - 57
d_22ens_2VALVALLEULEUEE60 - 11160 - 111
d_23ens_2PROPROPROPROEE118 - 213118 - 213
d_11ens_3VALVALSERSERCC1 - 251 - 25
d_12ens_3LEULEUTHRTHRCC49 - 10649 - 106
d_13ens_3GLYGLYCYSCYSCC118 - 146118 - 146
d_21ens_3VALVALCYSCYSFF1 - 1461 - 146

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.157058427019, 0.88831938912, 0.431533675878), (0.886678994264, -0.319254396215, 0.334480181219), (0.434894253392, 0.330098914587, -0.837795735818)-27.1008779925, 43.4538247781, -10.7614180794
2given(0.141210743599, 0.889105081826, 0.435375331596), (0.887436074556, -0.308600757094, 0.342378133499), (0.43876729535, 0.338020304407, -0.832601666068)-26.9877075507, 43.1250923888, -10.9298514323
3given(0.152278239414, 0.897999111132, 0.412806170263), (0.909435754212, -0.290845186145, 0.297213200679), (0.386959877458, 0.330161587866, -0.860961891802)-28.2982610789, 41.4250996094, -10.3601317717

-
Components

#1: Antibody Neutralizing antibody Fab fragment, heavy chain


Mass: 23681.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Neutralizing antibody Fab fragment, light chain


Mass: 22933.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein Leptin / Obese protein / Obesity factor


Mass: 15984.296 Da / Num. of mol.: 2 / Mutation: W100E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LEP, OB, OBS / Plasmid: pSUMO-TCS(A)-LEP W100E / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41159
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein at 25 mg/ml in 20 mM Hepes pH 7.4 and 75 mM sodium chloride versus a reservoir with 18% PEG 8,000 and 20% glycerol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20607 / % possible obs: 88.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 0.94 / CC star: 0.985 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.135 / Rrim(I) all: 0.2 / Χ2: 0.886 / Net I/σ(I): 5.2 / Num. measured all: 38063
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3-3.051.40.8838200.4780.8040.8491.2270.95566.5
3.05-3.111.50.6917700.4970.8150.6680.9620.99570.5
3.11-3.171.60.6678690.5690.8520.6480.9310.99376
3.17-3.231.60.6349510.3980.7550.6010.8750.90878.5
3.23-3.31.60.5829350.4240.7720.5510.8031.11783.2
3.3-3.381.70.47210100.6390.8830.4610.660.92488.7
3.38-3.461.80.45210710.7070.910.4230.6210.95189.4
3.46-3.561.80.36210140.7210.9150.340.4980.95988.8
3.56-3.661.80.39510560.6470.8860.360.5360.9191.2
3.66-3.781.90.31911200.7770.9350.2970.4370.98696.6
3.78-3.9120.29610960.7350.9210.2710.4030.97795.7
3.91-4.0720.20311450.8740.9660.1830.2740.87796.6
4.07-4.2620.18110630.9020.9740.160.2430.84294.5
4.26-4.4820.11411250.9340.9830.1010.1530.83493.4
4.48-4.761.90.09310330.9460.9860.0830.1250.86290.9
4.76-5.1320.09811240.9490.9870.0860.130.76997.3
5.13-5.642.10.09811120.9540.9880.0840.130.77396.9
5.64-6.4620.111050.9570.9890.0870.1330.76394.2
6.46-8.1320.06110910.9790.9950.0520.0810.85693.7
8.13-5020.03310970.9780.9940.030.0440.83995.1

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→40.17 Å / SU ML: 0.4652 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.3716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 1648 9.95 %
Rwork0.2363 14921 -
obs0.2403 16569 79.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.54 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 10 0 8152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268322
X-RAY DIFFRACTIONf_angle_d0.572311328
X-RAY DIFFRACTIONf_chiral_restr0.04481306
X-RAY DIFFRACTIONf_plane_restr0.00571442
X-RAY DIFFRACTIONf_dihedral_angle_d12.45212976
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.49022126529
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.623609139456
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS1.92833788222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.190.3943850.2923629X-RAY DIFFRACTION40.82
3.19-3.290.3589780.2972717X-RAY DIFFRACTION46.03
3.29-3.410.3257950.2843918X-RAY DIFFRACTION58.49
3.41-3.550.33391110.30381036X-RAY DIFFRACTION66.92
3.55-3.710.32361460.27951308X-RAY DIFFRACTION82.43
3.71-3.910.30461650.2741443X-RAY DIFFRACTION94.92
3.91-4.150.30341620.24631504X-RAY DIFFRACTION96.02
4.15-4.470.25711610.21361477X-RAY DIFFRACTION93.76
4.47-4.920.22471600.18591435X-RAY DIFFRACTION93.17
4.92-5.630.24421670.2161508X-RAY DIFFRACTION96.93
5.63-7.080.30491620.25541445X-RAY DIFFRACTION92.73
7.09-40.170.23211560.20441501X-RAY DIFFRACTION95.84

+
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