SAXSdb — 9v1h

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1. Structure Basics

entry_id	9v1h
deposition_date	2025-05-19
title	Cryo-EM structure of Gi-coupled NPFF2R in complex with GUB08248
keywords	NPFF2R, Prolactin-releasing peptide, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	38.77 Å
rg_electron	38.71 Å
i0	235833000.00
molecular_weight	126420.0 kDa
excluded_volume	159030 Å³
envelope_volume	216440 Å³
shell_volume	47621 Å³
envelope_diameter	131.5 Å
shell_rg	42.81 Å
envelope_rg	39.19 Å
shape_rg	38.72 Å
total_rg	38.96 Å
total_atoms	8890
n_residues	1140
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	128.1 Å
rg_real	38.82 Å
rg_real_error	1.12 Å
i0_real	2.3580e+08
i0_real_error	4.7680e+06
rg_reciprocal	38.80 Å
i0_reciprocal	235800000.0000
total_estimate	0.8880
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.6 Å
skewness	0.274
kurtosis	-0.586
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	43250000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(s) subunit alpha-1
formula_weight	41641.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8890

MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDVTDIIIKMNLRDCGLF

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	40227.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSGVSGWRLFKKIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	scFv16
formula_weight	26277.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7729.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 5 polymer

description	GUB08248
formula_weight	1234.5 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SRGKRPVGRFA

Entity 6 polymer

description	Neuropeptide FF receptor 2
formula_weight	48734.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MNEKWDTNSSENWHPIWNVNDTKHHLYSDINITYVNYYLHQPQVAAIFIISYFLIFFLCMMGNTVVCFIVMRNKHMHTVTNLFILNLAISDLLVGIFCMPITLLDNIIAGWPFGNTMCKISGLVQGISVAASVFTLVAIAVDRFQCVVYPFKPKLTIKTAFVIIMIIWVLAITIMSPSAVMLHVQEEKYYRVRLNSQNKTSPVYWCREDWPNQEMRKIYTTVLFANIYLAPLSLIVIMYGRIGISLFRAAVPHTGRKNQEQWHVVSRKKQKIIKMLLIVALLFILSWLPLWTLMMLSDYADLSPNELQIINIYIYPFAHWLAFGNSSVNPIIYGFFNENFRRGFQEAFQLQLCQKRAKPMEAYALKAKSHVLINTSNQLVQESTFQNPHGETLLYRKSAEKPQQELVMEELKETTNSSEI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.85 Å
resolution_method	—
num_particles	324707

fit	/app/data/saxs_computation/v1/9v1h/9v1h.fit
pddf	/app/data/pr_computation/v1/9v1h/9v1h.pr.out
profile	/app/data/saxs_computation/v1/9v1h/9v1h.dat

Cryo-EM structure of Gi-coupled NPFF2R in complex with GUB08248

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)