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- EMDB-41233: Complex of NPR1 ectodomain with ANP plus an allosteric activating... -

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Basic information

Entry
Database: EMDB / ID: EMD-41233
TitleComplex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Map data
Sample
  • Complex: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
    • Protein or peptide: REGN5381 Fab heavy chain
    • Protein or peptide: REGN5381 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAtrial natriuretic peptide / antibody / activator / pulmonary hypertension / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / peptide receptor activity / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity ...positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / peptide receptor activity / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / guanylate cyclase / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / guanylate cyclase activity / Physiological factors / regulation of vascular permeability / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hormone binding / positive regulation of urine volume / negative regulation of JUN kinase activity / sodium ion export across plasma membrane / neuropeptide hormone activity / G protein-coupled peptide receptor activity / cardiac muscle hypertrophy in response to stress / negative regulation of systemic arterial blood pressure / hormone receptor binding / aortic valve morphogenesis / adenylate cyclase activity / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / response to muscle stretch / blood vessel diameter maintenance / negative regulation of angiogenesis / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / hormone activity / negative regulation of cell growth / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / cell surface receptor signaling pathway / receptor complex / protein kinase activity / Amyloid fiber formation / signaling receptor binding / GTP binding / protein-containing complex / extracellular space / extracellular region / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. ...Natriuretic peptide, atrial type / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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: 3.08 Å
AuthorsFranklin MC / Romero Hernandez A
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Authors: Franklin MC / Romero Hernandez A
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41233.png

Downloads & links

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Map

FileDownload / File: emd_41233.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 310 pix.
= 266.6 Å		0.86 Å/pix.
x 310 pix.
= 266.6 Å		0.86 Å/pix.
x 310 pix.
= 266.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.537
Minimum - Maximum-4.216814 - 6.196395
Average (Standard dev.)0.0017459996 (±0.14021935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 266.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41233_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_41233_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 : Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab

EntireName: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
Components
  • Complex: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: Atrial natriuretic peptide
    • Protein or peptide: REGN5381 Fab heavy chain
    • Protein or peptide: REGN5381 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab

SupramoleculeName: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
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: 52.263723 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GNLTVAVVLP LANTSYPWSW ARVGPAVELA LAQVKARPDL LPGWTVRTVL GSSENALGVC SDTAAPLAAV DLKWEHNPAV FLGPGCVYA AAPVGRFTAH WRVPLLTAGA PALGFGVKDE YALTTRAGPS YAKLGDFVAA LHRRLGWERQ ALMLYAYRPG D EEHCFFLV ...String:
GNLTVAVVLP LANTSYPWSW ARVGPAVELA LAQVKARPDL LPGWTVRTVL GSSENALGVC SDTAAPLAAV DLKWEHNPAV FLGPGCVYA AAPVGRFTAH WRVPLLTAGA PALGFGVKDE YALTTRAGPS YAKLGDFVAA LHRRLGWERQ ALMLYAYRPG D EEHCFFLV EGLFMRVRDR LNITVDHLEF AEDDLSHYTR LLRTMPRKGR VIYICSSPDA FRTLMLLALE AGLCGEDYVF FH LDIFGQS LQGGQGPAPR RPWERGDGQD VSARQAFQAA KIITYKDPDN PEYLEFLKQL KHLAYEQFNF TMEDGLVNTI PAS FHDGLL LYIQAVTETL AHGGTVTDGE NITQRMWNRS FQGVTGYLKI DSSGDRETDF SLWDMDPENG AFRVVLNYNG TSQE LVAVS GRKLNWPLGY PPPDIPKCGF DNEDPACNQD HLSTLEEQKL ISEEDLGGEQ KLISEEDLHH HHHH

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
SequenceString:
SLRRSSCFGG RMDRIGAQSG LGCNSFRY

UniProtKB: Natriuretic peptides A

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Macromolecule #3: REGN5381 Fab heavy chain

MacromoleculeName: REGN5381 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: Velocimmune mouse
Molecular weightTheoretical: 24.81877 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGASVTV SCKASGYTFT DYYMHWVRQA PGQGLEWMGW IKPNSGGTNS AQRFQGRITM TWDTSISTAY MELSRLRSD DTAVYYCSRG GPVMNYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VKKPGASVTV SCKASGYTFT DYYMHWVRQA PGQGLEWMGW IKPNSGGTNS AQRFQGRITM TWDTSISTAY MELSRLRSD DTAVYYCSRG GPVMNYYYYY GMDVWGQGTT VTVSSASTKG PSVFPLAPCS RSTSESTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTKTYTCN VDHKPSNTKV DKRVESKYGP P

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Macromolecule #4: REGN5381 Fab light chain

MacromoleculeName: REGN5381 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: Velocimmune mouse
Molecular weightTheoretical: 23.323898 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
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 #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

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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

Concentration1.6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1299989
Startup modelType of model: NONE / Details: cryoSPARC ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 682951
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6

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