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Yorodumi- EMDB-41233: Complex of NPR1 ectodomain with ANP plus an allosteric activating... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41233 | |||||||||
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Title | Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Atrial 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 / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / neuropeptide receptor binding / positive regulation of renal sodium excretion / 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 / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / neuropeptide receptor binding / positive regulation of renal sodium excretion / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / hormone binding / regulation of vascular permeability / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / negative regulation of JUN kinase activity / sodium ion export across plasma membrane / positive regulation of urine volume / neuropeptide hormone activity / cardiac muscle hypertrophy in response to stress / G protein-coupled peptide receptor activity / hormone receptor binding / negative regulation of systemic arterial blood pressure / adenylate cyclase activity / aortic valve morphogenesis / cGMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / response to muscle stretch / negative regulation of angiogenesis / blood vessel diameter maintenance / 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 / receptor complex / cell surface receptor signaling pathway / 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 | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Franklin MC / Romero Hernandez A | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381 Authors: Franklin MC / Romero Hernandez A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41233.map.gz | 107.1 MB | EMDB map data format | |
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Header (meta data) | emd-41233-v30.xml emd-41233.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_41233.png | 107 KB | ||
Filedesc metadata | emd-41233.cif.gz | 6.2 KB | ||
Others | emd_41233_half_map_1.map.gz emd_41233_half_map_2.map.gz | 105.4 MB 105.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41233 | HTTPS FTP |
-Validation report
Summary document | emd_41233_validation.pdf.gz | 936.1 KB | Display | EMDB validaton report |
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Full document | emd_41233_full_validation.pdf.gz | 935.7 KB | Display | |
Data in XML | emd_41233_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_41233_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41233 | HTTPS FTP |
-Related structure data
Related structure data | 8tg9MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41233.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41233_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41233_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
Entire | Name: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab |
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Components |
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-Supramolecule #1: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
Supramolecule | Name: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Atrial natriuretic peptide receptor 1
Macromolecule | Name: Atrial natriuretic peptide receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: guanylate cyclase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 52.263723 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #2: Atrial natriuretic peptide
Macromolecule | Name: Atrial natriuretic peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.087505 KDa |
Sequence | String: SLRRSSCFGG RMDRIGAQSG LGCNSFRY UniProtKB: Natriuretic peptides A |
-Macromolecule #3: REGN5381 Fab heavy chain
Macromolecule | Name: REGN5381 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: Velocimmune mouse |
Molecular weight | Theoretical: 24.81877 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #4: REGN5381 Fab light chain
Macromolecule | Name: REGN5381 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: Velocimmune mouse |
Molecular weight | Theoretical: 23.323898 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |