SAXSdb — 9vif

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1. Structure Basics

entry_id	9vif
deposition_date	2025-06-18
title	Cryo-EM Structure of NPFFR1 in complex with peptide NPFF
keywords	GPCR, NPFFR1, 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	40.19 Å
rg_electron	40.21 Å
i0	249040000.00
molecular_weight	128680.0 kDa
excluded_volume	161370 Å³
envelope_volume	229290 Å³
shell_volume	49404 Å³
envelope_diameter	136.9 Å
shell_rg	43.43 Å
envelope_rg	39.88 Å
shape_rg	40.22 Å
total_rg	40.37 Å
total_atoms	9038
n_residues	1149
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	132.8 Å
rg_real	40.18 Å
rg_real_error	0.97 Å
i0_real	2.4900e+08
i0_real_error	4.4650e+06
rg_reciprocal	40.19 Å
i0_reciprocal	249000000.0000
total_estimate	0.8946
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.1 Å
skewness	0.221
kurtosis	-0.621
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	38510000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.915

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Neuropeptide FF receptor 1
formula_weight	35150.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9038

NLTFSSYYQHTSPVAAMFIVAYALIFLLCMVGNTLVCFIVLKNRHMHTVTNMFILNLAVSDLLVGIFCMPTTLVDNLITGWPFDNATCKMSGLVQGMSVSASVWTLVAIAVERFRCIVHPFREKLTLRKALVTIAVIWALALLIMCPSAVTLTVTREEHHFMVDARNRSYPLYSCWEAWPEKGMRRVYTTVLFSHIYLAPLALIVVMYARIARKLCQAPGPAPGGEEAADPRASRRRARVVHMLVMVALFFTLSWLPLWALLLLIDYGQLSAPQLHLVTVYAFPFAHWLAFFNSSANPIIYGYFNENFRR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	Guanine nucleotide-binding protein G(i) subunit alpha-1
formula_weight	39966.4 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	37198.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
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	5931.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 5 polymer

description	scFv16
formula_weight	26466.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 6 polymer

description	NPFF
formula_weight	1154.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

FLFQPQRFA

Source

organism	Homo sapiens
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	3.190 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.19 Å
resolution_method	—
num_particles	270038

fit	/app/data/saxs_computation/vi/9vif/9vif.fit
pddf	/app/data/pr_computation/vi/9vif/9vif.pr.out
profile	/app/data/saxs_computation/vi/9vif/9vif.dat

Cryo-EM Structure of NPFFR1 in complex with peptide NPFF

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

Refinement

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

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)