SAXSdb — 9umr

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1. Structure Basics

entry_id	9umr
deposition_date	2025-04-22
last_revision	2025-11-26
title	Structure of C5a-pep bound human C5aR1 in complex with Go
keywords	GPCR, G protein, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex; SIGNALING 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	38.82 Å
rg_electron	38.85 Å
i0	205571000.00
molecular_weight	116770.0 kDa
excluded_volume	146410 Å³
envelope_volume	209490 Å³
shell_volume	46505 Å³
envelope_diameter	132.2 Å
shell_rg	42.73 Å
envelope_rg	38.41 Å
shape_rg	38.83 Å
total_rg	39.16 Å
total_atoms	8235
n_residues	1120
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	127.1 Å
rg_real	38.77 Å
rg_real_error	1.01 Å
i0_real	2.0560e+08
i0_real_error	3.3810e+06
rg_reciprocal	38.81 Å
i0_reciprocal	205600000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.188
kurtosis	-0.625
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	31870000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.903

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Muscarinic acetylcholine receptor M4,C5a anaphylatoxin chemotactic receptor 1
formula_weight	45273.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	8235

MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSDSFNYTTPDYGHYDDKDTLDLNTPVDKTSNTLRVPDILALVIFAVVFLVGVLGNALVVWVTAFEAKRTINAIWFLNLAVADFLSCLALPILFTSIVQHHHWPFGGAACSILPSLILLNMYASILLLATISADRFLLVFKPIWCQNFRGAGLAWIACAVAWGLALLLTIPSFLYRVVREEYFPPKVLCGVDYSHDKRRERAVAIVRLVLGFLWPLLTLTICYTFILLRTWSRRATRSTKTLKVVVAVVASFFIFWLPYQVTGIMMSFLEPSSPTFLLLKKLDSLCVSFAYINCCINPIIYVVAGQGFQGRLRKSLPSLLRNVLTEESVVRESKSFTRSTVDTMAQKTQAV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mus musculus

Entity 2 polymer

description	Guanine nucleotide-binding protein G(o) subunit alpha
formula_weight	28193.9 kDa
ec_number	3.6.5.-
mutation	G42D,E43N,A227D,G230D,I332A,V335I
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKSTIVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIFCVDLSDYDQVLHEDETTNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	38534.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Antibody fragment - ScFv16
formula_weight	26466.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELK

Source

organism	Mus musculus
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 6 polymer

description	C5a-pep ligand
formula_weight	869.1 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

FKPAAR

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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	3.15 Å
resolution_method	—
num_particles	918121

fit	/app/data/saxs_computation/um/9umr/9umr.fit
pddf	/app/data/pr_computation/um/9umr/9umr.pr.out
profile	/app/data/saxs_computation/um/9umr/9umr.dat

Structure of C5a-pep bound human C5aR1 in complex with Go

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

Source

Entity 6 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)