[English] 日本語
Yorodumi
- PDB-6w4v: Structure of anti-ferroportin Fab45D8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w4v
TitleStructure of anti-ferroportin Fab45D8
Components
  • Fab45D8 Heavy Chain
  • Fab45D8 Light Chain
KeywordsIMMUNE SYSTEM / ferroportin / transporter / iron / hepcidin / antibody / Fab
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBillesboelle, C.B. / Azumaya, C.M. / Gonen, S. / Powers, A. / Kretsch, R.C. / Schneider, S. / Arvedson, T. / Dror, R.O. / Cheng, Y. / Manglik, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1DP5OD023048 United States
CitationJournal: Nature / Year: 2020
Title: Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms.
Authors: Christian B Billesbølle / Caleigh M Azumaya / Rachael C Kretsch / Alexander S Powers / Shane Gonen / Simon Schneider / Tara Arvedson / Ron O Dror / Yifan Cheng / Aashish Manglik /
Abstract: The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin regulates iron absorption and recycling by inducing ...The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin regulates iron absorption and recycling by inducing the internalization and degradation of ferroportin. Aberrant ferroportin activity can lead to diseases of iron overload, such as haemochromatosis, or iron limitation anaemias. Here we determine cryogenic electron microscopy structures of ferroportin in lipid nanodiscs, both in the apo state and in complex with hepcidin and the iron mimetic cobalt. These structures and accompanying molecular dynamics simulations identify two metal-binding sites within the N and C domains of ferroportin. Hepcidin binds ferroportin in an outward-open conformation and completely occludes the iron efflux pathway to inhibit transport. The carboxy terminus of hepcidin directly contacts the divalent metal in the ferroportin C domain. Hepcidin binding to ferroportin is coupled to iron binding, with an 80-fold increase in hepcidin affinity in the presence of iron. These results suggest a model for hepcidin regulation of ferroportin, in which only ferroportin molecules loaded with iron are targeted for degradation. More broadly, our structural and functional insights may enable more targeted manipulation of the hepcidin-ferroportin axis in disorders of iron homeostasis.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
D: Fab45D8 Light Chain
C: Fab45D8 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7257
Polymers48,4152
Non-polymers3105
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-16 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.097, 36.907, 86.514
Angle α, β, γ (deg.)90.000, 112.989, 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

-
Components

#1: Antibody Fab45D8 Light Chain


Mass: 24008.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Protein Fab45D8 Heavy Chain


Mass: 24406.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.3 M trimethylamine-N-oxide (TMAO), 0.1 M Tris, pH 8.5, 30% w/v PEG2000 MME

-
Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→39.82 Å / Num. obs: 24736 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 43.19 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 1832 / CC1/2: 0.3

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BZV

6bzv


Resolution: 2.1→39.82 Å / SU ML: 0.2785 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 836 3.39 %
Rwork0.2157 23834 -
obs0.2168 24670 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 20 125 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583460
X-RAY DIFFRACTIONf_angle_d0.91794719
X-RAY DIFFRACTIONf_chiral_restr0.0541533
X-RAY DIFFRACTIONf_plane_restr0.0047599
X-RAY DIFFRACTIONf_dihedral_angle_d18.12271229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.34611140.31163476X-RAY DIFFRACTION86.26
2.23-2.410.32731410.29664009X-RAY DIFFRACTION99.4
2.41-2.650.34961420.28214040X-RAY DIFFRACTION99.88
2.65-3.030.27551400.25194047X-RAY DIFFRACTION99.98
3.03-3.820.23951470.21944058X-RAY DIFFRACTION99.95
3.82-39.820.20551520.16934204X-RAY DIFFRACTION99.89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57887108020.881026657864-0.1025497107461.080560381810.1995168937462.239798470930.0469429361564-0.6369283535050.4028387843170.2648992984910.1635214997470.004750745781690.1026674496460.10141783670.1989041322720.590139048730.1115622942880.02197533742430.648221622811-0.1757011311890.4539997579710.4717584319652.2925767085232.8595380407
24.64432639164-1.181588223270.2245941572091.57635251324-0.1358041027332.05539361862-0.155991842533-0.4598323230630.7100330428340.08408249886970.127166949199-0.548286551854-0.07127498310680.201619820211-0.08178577612110.3394818400850.0345261994862-0.02878288178830.319301154365-0.03923858324940.40861932475733.1876608585-10.270918972219.5668090114
31.48115281261-0.89702693469-0.6721963248451.116989214040.3197009428761.03419288953-0.08356928397430.0283305804274-0.1884508006630.0676753210744-0.00486840825260.0990256926350.08016328325410.08534838726551.29886128466E-90.2809937026910.01979925114440.01972158858280.3607677577130.04557065002340.330699151293-6.65154350154-4.2736994174713.140088127
41.85698848869-1.36509781054-0.2600547845610.9756479220671.315498694011.20279853097-0.123640319327-0.0344188128260.2909876777270.09975532096220.1755246364140.1457898225070.215582734035-0.04326601626750.02622686721860.337278989060.03630620076370.01659695101980.3481755434550.06441865421250.369874001691-3.76915803927-3.9413068258211.3342727561
50.408118790233-0.19013976039-0.1947266205950.359858464399-0.2158852010620.601166521153-0.3936136584950.1633689668170.3430005551390.321866700812-0.510700006048-0.693299849474-0.1686195029010.574699024177-0.03737035594910.4404266692750.0718067173299-0.09471307002790.4231855381320.02915194498770.46379444066134.378868908-23.981547088816.2032241502
63.47268311261-0.790353811329-0.05487240618161.31196421168-0.2628105873780.3603192799710.1103420106030.0508281252592-0.4677828621970.075242400941-0.008823123843210.1384223173030.17382659104-0.023533752837-0.003601480987440.4122137196050.00530397986987-0.05283669098930.2649052515840.02711142070910.38528104114222.9144539628-21.654072659213.8597526399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 105 )
2X-RAY DIFFRACTION2chain 'D' and (resid 106 through 218 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 59 )
4X-RAY DIFFRACTION4chain 'C' and (resid 60 through 124 )
5X-RAY DIFFRACTION5chain 'C' and (resid 125 through 139 )
6X-RAY DIFFRACTION6chain 'C' and (resid 140 through 220 )

+
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://pdbjlvh1.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