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- EMDB-47330: Human GC-A bound to ANP and REGN5308 -

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Basic information

Entry
Database: EMDB / ID: EMD-47330
TitleHuman GC-A bound to ANP and REGN5308
Map data
Sample
  • Complex: RGN5308 bound to NPR1-ANP
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
    • Protein or peptide: REGN5308 - Heavy chain
    • Protein or peptide: REGN5308 - Light chain
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsreceptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway ...negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / receptor guanylyl cyclase signaling pathway / body fluid secretion / positive regulation of potassium ion export across plasma membrane / peptide receptor activity / positive regulation of renal sodium excretion / cell growth involved in cardiac muscle cell development / guanylate cyclase / synaptic signaling via neuropeptide / cGMP biosynthetic process / negative regulation of JUN kinase activity / guanylate cyclase activity / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / sodium ion export across plasma membrane / regulation of vascular permeability / neuropeptide hormone activity / positive regulation of urine volume / hormone receptor binding / negative regulation of systemic arterial blood pressure / glycinergic synapse / cardiac muscle hypertrophy in response to stress / G protein-coupled peptide receptor activity / aortic valve morphogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / : / dopamine metabolic process / hormone binding / peptide hormone binding / brush border / cellular response to angiotensin / neuropeptide signaling pathway / positive regulation of heart rate / response to muscle stretch / positive regulation of cardiac muscle contraction / negative regulation of angiogenesis / blood vessel diameter maintenance / cell projection / negative regulation of smooth muscle cell proliferation / female pregnancy / cellular response to mechanical stimulus / hormone activity / negative regulation of cell growth / response to insulin / regulation of blood pressure / vasodilation / cellular response to hydrogen peroxide / protein folding / : / perikaryon / response to hypoxia / cell surface receptor signaling pathway / protein kinase activity / receptor complex / Amyloid fiber formation / signaling receptor binding / GTP binding / perinuclear region of cytoplasm / protein-containing complex / extracellular space / extracellular region / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : ...Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Natriuretic peptides A / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu S / Huang X-Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: human NPR1 bound to ANP and RGN5308
Authors: Liu S / Huang X-Y
History
DepositionOct 16, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47330.png

Downloads & links

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Map

FileDownload / File: emd_47330.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.6
Minimum - Maximum-4.2230277 - 7.1407776
Average (Standard dev.)0.00047232604 (±0.14201224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47330_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47330_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RGN5308 bound to NPR1-ANP

EntireName: RGN5308 bound to NPR1-ANP
Components
  • Complex: RGN5308 bound to NPR1-ANP
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
    • Protein or peptide: REGN5308 - Heavy chain
    • Protein or peptide: REGN5308 - Light chain
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: RGN5308 bound to NPR1-ANP

SupramoleculeName: RGN5308 bound to NPR1-ANP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Atrial natriuretic peptide receptor 1

MacromoleculeName: Atrial natriuretic peptide receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: guanylate cyclase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115.702828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AAGNLTVAVV LPLANTSYPW SWARVGPAVE LALAQVKARP DLLPGWTVRT VLGSSENALG VCSDTAAPLA AVDLKWEHNP AVFLGPGCV YAAAPVGRFT AHWRVPLLTA GAPALGFGVK DEYALTTRAG PSYAKLGDFV AALHRRLGWE RQALMLYAYR P GDEEHCFF ...String:
AAGNLTVAVV LPLANTSYPW SWARVGPAVE LALAQVKARP DLLPGWTVRT VLGSSENALG VCSDTAAPLA AVDLKWEHNP AVFLGPGCV YAAAPVGRFT AHWRVPLLTA GAPALGFGVK DEYALTTRAG PSYAKLGDFV AALHRRLGWE RQALMLYAYR P GDEEHCFF LVEGLFMRVR DRLNITVDHL EFAEDDLSHY TRLLRTMPRK GRVIYICSSP DAFRTLMLLA LEAGLCGEDY VF FHLDIFG QSLQGGQGPA PRRPWERGDG QDVSARQAFQ AAKIITYKDP DNPEYLEFLK QLKHLAYEQF NFTMEDGLVN TIP ASFHDG LLLYIQAVTE TLAHGGTVTD GENITQRMWN RSFQGVTGYL KIDSSGDRET DFSLWDMDPE NGAFRVVLNY NGTS QELVA VSGRKLNWPL GYPPPDIPKC GFDNEDPACN QDHLSTLEVL ALVGSLSLLG ILIVSFFIYR KMQLEKELAS ELWRV RWED VEPSSLERHL RSAGSRLTLS GRGSNYGSLL TTEGQFQVFA KTAYYKGNLV AVKRVNRKRI ELTRKVLFEL KHMRDV QNE HLTRFVGACT DPPNICILTE YCPRGSLQDI LENESITLDW MFRYSLTNDI VKGMLFLHNG AICSHGNLKS SNCVVDG RF VLKITDYGLE SFRDLDPEQG HTVYAKKLWT APELLRMASP PVRGSQAGDV YSFGIILQEI ALRSGVFHVE GLDLSPKE I IERVTRGEQP PFRPSLALQS HLEELGLLMQ RCWAEDPQER PPFQQIRLTL RKFNRENSSN ILDNLLSRME QYANNLEEL VEERTQAYLE EKRKAEALLY QILPHSVAEQ LKRGETVQAE AFDSVTIYFS DIVGFTALSA ESTPMQVVTL LNDLYTCFDA VIDNFDVYK VETIGDAYMV VSGLPVRNGR LHACEVARMA LALLDAVRSF RIRHRPQEQL RLRIGIHTGP VCAGVVGLKM P RYCLFGDT VNTASRMESN GEALKIHLSS ETKAVLEEFG GFELELRGDV EMKGKGKVRT YWLLGERGSS TRG

UniProtKB: Atrial natriuretic peptide receptor 1

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Macromolecule #2: Atrial natriuretic peptide

MacromoleculeName: Atrial natriuretic peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.087505 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLRRSSCFGG RMDRIGAQSG LGCNSFRY

UniProtKB: Natriuretic peptides A

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Macromolecule #3: REGN5308 - Heavy chain

MacromoleculeName: REGN5308 - Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.46842 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QVQLVQSGAE VKKPGASVTV SCKASGYTFT DYYMHWVRQA PGQGLEWMGW IKPNSGGTNS AQRFQGRITM TWDTSISTAY MELSRLRSD DTAVYYCSRG GPVMNYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGASVTV SCKASGYTFT DYYMHWVRQA PGQGLEWMGW IKPNSGGTNS AQRFQGRITM TWDTSISTAY MELSRLRSD DTAVYYCSRG GPVMNYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSC

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Macromolecule #4: REGN5308 - Light chain

MacromoleculeName: REGN5308 - Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.323898 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NIQMTQSPSS LSASVGDRVT ITCRASQSID SYLNWYQQKP GKAPKLLIYV ASSLQSGVPS RFSGSGSGKD FTLTISSLQP EDFATYYCQ QSYSIPTFGQ GTRLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
NIQMTQSPSS LSASVGDRVT ITCRASQSID SYLNWYQQKP GKAPKLLIYV ASSLQSGVPS RFSGSGSGKD FTLTISSLQP EDFATYYCQ QSYSIPTFGQ GTRLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #7: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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