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- EMDB-47329: Human GC-A bound to XX16 -

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Basic information

Entry
Database: EMDB / ID: EMD-47329
TitleHuman GC-A bound to XX16
Map data
Sample
  • Complex: Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with Fab fragment
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: XX16 - Heavy Chain
    • Protein or peptide: XX16 - Light chain
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordsreceptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


ANPR-A receptor complex / natriuretic peptide receptor activity / : / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity ...ANPR-A receptor complex / natriuretic peptide receptor activity / : / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / positive regulation of renal sodium excretion / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / Physiological factors / regulation of vascular permeability / positive regulation of urine volume / G protein-coupled peptide receptor activity / : / dopamine metabolic process / hormone binding / peptide hormone binding / negative regulation of angiogenesis / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / negative regulation of cell growth / regulation of blood pressure / cell surface receptor signaling pathway / protein kinase activity / receptor complex / GTP binding / ATP binding / plasma membrane
Similarity search - Function
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 ...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
Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 XX16
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_47329.png

Downloads & links

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Map

FileDownload / File: emd_47329.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.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.9288893 - 7.4779205
Average (Standard dev.)0.0011739763 (±0.12462338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47329_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_47329_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 : Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with...

EntireName: Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with Fab fragment
Components
  • Complex: Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with Fab fragment
    • Protein or peptide: Atrial natriuretic peptide receptor 1
    • Protein or peptide: XX16 - Heavy Chain
    • Protein or peptide: XX16 - Light chain
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with...

SupramoleculeName: Complex of Guanylyl Cyclase-A/Natriuretic peptide receptor A with Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 115.560688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 HLSTLEVLAL VGSLSLLGIL IVSFFIYRKM QLEKELASEL WRVRW EDVE PSSLERHLRS AGSRLTLSGR GSNYGSLLTT EGQFQVFAKT AYYKGNLVAV KRVNRKRIEL TRKVLFELKH MRDVQN EHL TRFVGACTDP PNICILTEYC PRGSLQDILE NESITLDWMF RYSLTNDIVK GMLFLHNGAI CSHGNLKSSN CVVDGRF VL KITDYGLESF RDLDPEQGHT VYAKKLWTAP ELLRMASPPV RGSQAGDVYS FGIILQEIAL RSGVFHVEGL DLSPKEII E RVTRGEQPPF RPSLALQSHL EELGLLMQRC WAEDPQERPP FQQIRLTLRK FNRENSSNIL DNLLSRMEQY ANNLEELVE ERTQAYLEEK RKAEALLYQI LPHSVAEQLK RGETVQAEAF DSVTIYFSDI VGFTALSAES TPMQVVTLLN DLYTCFDAVI DNFDVYKVE TIGDAYMVVS GLPVRNGRLH ACEVARMALA LLDAVRSFRI RHRPQEQLRL RIGIHTGPVC AGVVGLKMPR Y CLFGDTVN TASRMESNGE ALKIHLSSET KAVLEEFGGF ELELRGDVEM KGKGKVRTYW LLGERGSSTR G

UniProtKB: Atrial natriuretic peptide receptor 1

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Macromolecule #2: XX16 - Heavy Chain

MacromoleculeName: XX16 - Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.483457 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QVQLLESGGG LVQPGGSLRL SCAASGFTFS SYWMNWVRQA PGKGLEWVSV IESKGNYIFY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD RYSMIYSYGA GAFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QVQLLESGGG LVQPGGSLRL SCAASGFTFS SYWMNWVRQA PGKGLEWVSV IESKGNYIFY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD RYSMIYSYGA GAFDYWGQGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC

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Macromolecule #3: XX16 - Light chain

MacromoleculeName: XX16 - Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.450102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QTWRKPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQGIS SYLAWYQQKP GKAPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QTWRKPRTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #6: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 2 / 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: 51.0 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 505000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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