SAXSdb — 9r78

▼

1. Structure Basics

entry_id	9r78
deposition_date	2025-05-14
title	Human Adenovirus D 10 Capsid Structure
keywords	virus, adenovirus, capsid, conjunctivitis; VIRUS
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	82.45 Å
rg_electron	82.39 Å
i0	28962900000.00
molecular_weight	1434500.0 kDa
excluded_volume	1784400 Å³
envelope_volume	2697700 Å³
shell_volume	262100 Å³
envelope_diameter	345.1 Å
shell_rg	85.98 Å
envelope_rg	82.84 Å
shape_rg	82.37 Å
total_rg	82.49 Å
total_atoms	198096
n_residues	12737
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

▼

3. P(r) Analysis (GNOM)

dmax	226.8 Å
rg_real	79.32 Å
rg_real_error	0.62 Å
i0_real	2.7700e+10
i0_real_error	4.9920e+08
rg_reciprocal	82.09 Å
i0_reciprocal	28930000000.0000
total_estimate	0.8954
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	95.5 Å
skewness	0.221
kurtosis	-0.442
angular_range	— – 0.0950 Å⁻¹
current_alpha	1.2960
highest_alpha	2767000000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.993; Stabil: 0.967; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.009

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Pre-protein VI
formula_weight	25546.1 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	1,2,3,4,5,6,7,8
atom_count	198096

MEDINFASLAPRHGTRPFMGTWNEIGTSQLNGGAFNWSSVWSGLKNFGSTLRTYGNKAWNSSTGQLLREKLKDQNFQQKVVDGLASGINGVVDIANQAVQREINSRLDPRPPTVVEMEDATLPPPKGEKRPRPDAEETILQVDEPPSYEEAVKAGMPTTRIIAPLATGVMKPATLDLPPPPAPAPPKATPVVQAPPVATAVRRVPARRQAQNWQSTLHSIVGLGVKSLKRRRCY

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

Entity 2 polymer

description	Hexon protein
formula_weight	106268.4 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L

MMPQWAYMHIAGQDASEYLSPGLVQFARATDTYFSLGNKFRNPTVAPTHDVTTDRSQRLTLRFVPVDREDTTYSYKARFTLAVGDNRVLDMASTYFDIRGVLDRGPSFKPYSGTAYNSLAPKSAPNPSQWTANEKQTGGQPKSVTQTFGSAPMGGSNITIEGLVIGTKEEEGNATEEIFADKTFQPEPQVGEENWQETEAFYGGRALKKDTKMKPCYGSFARPTNEKGGQAKLKLNDQGQPTKDYDIDLAFFDTPGGTPPTGSGQQEEYKADIVMYTENVNLETPDTHVVYKPGKEDESSETNLTQQSMPNRPNYIGFRDNFVGLMYYNSTGNMGVLAGQASQLNAVVDLQDRNTELSYQLLLDSLGDRTRYFSMWNSAVDSYDPDVRIIENHGVEDELPNYCFPLNGTGTNSTYQGVKVKTGQDGAEETEWDKDETVARQNQIAKGNVYAMEINLQANLWKSFLYSNVALYLPDSYKYTPANVTLPANTNTYEYMNGRVVAPSLVDAYINIGARWSLDPMDNVNPFNHHRNAGLRYRSMLLGNGRYVPFHIQVPQKFFAIKNLLLLPGSYTYEWNFRKDVNMILQSSLGNDLRVDGASVRFDSVNLYATFFPMAHNTASTLEAMLRNDTNDQSFNDYLSAANMLYPIPAKATNVPISIPSRNWAAFRGWSFTRLKTKETPSLGSGFDPYFVYSGSIPYLDGTFYLNHTFKKVSIMFDSSVSWPGNDRLLTPNEFEIKRSVDGEGYNVAQCNMTKDWFLVQMLSHYNIGYQGFHVPEGYKDRMYSFFRNFQPMSRQVVDEINYKDYKAVTLPFQHNNSGFTGYLAPTMRQGQPYPANFPYPLIGQTAVPSVTQKKFLCDRVMWRIPFSSNFMSMGALTDLGQNMLYANSAHALDMTFEVDPMDEPTLLYLLFEVFDVVRVHQPHRGVIEAVYLRTPFSAGN

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

Entity 3 polymer

description	Penton protein
formula_weight	58631.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MRRAVVSSSPPPSYESVMAQATLEVPFVPPRYMAPTEGRNSIRYSELAPQYDTTRVYLVDNKSADIASLNYQNDHSNFLTTVVQNNDFTPAEASTQTINFDERSRWGGDLKTILHTNMPNVNEYMFTSKFKARVMVARKHPEGVVETDLSQDKLEYEWFEFTLPEGNFSETMTIDLMNNAILENYLQVGRQNGVLESDIGVKFDSRNFKLGWDPVTKLVMPGVYTYEAFHPDVVLLPGCGVDFTESRLSNLLGIRKKQPFQEGFRIMYEDLEGGNIPALLDVPKYLESKKKVEDETKNAAAATADTTTRGDTFATPAQETAADKKVEVLPIEKDESGRSYNLIQGTHDTLYRSWYLSYTYGDPEKGVQSWTLLTTPDVTCGAEQVYWSLPDLMQDPVTFRSTQQVSNYPVVGAELMPFRAKSFYNDLAVYSQLIRSYTSLTHVFNRFPDNQILCRPPAPTITTVSENVPALTDHGTLPLRSSIRGVQRVTVTDARRRTCPYVYKALGIVAPRVLSSRTF

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

Entity 4 polymer

description	Pre-hexon-linking protein IIIa
formula_weight	62170.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MQQAPDPAIRAALQSQPSGIASDDWEAAMQRIMALTTRNPESFRQQPQANRLSAILEAVVPSRTNPTHEKVLAIVNALAENKAIRPDEAGLVYNALLERVGRYNSTNVQSNLDRLVTDVREAVAQRERFKNEGLGSLVALNAFLATQPANVPRGQDDYTNFISALRLMVTEVPQSEVYQSGPDYFFQTSRQGLQTVNLSQAFKNLRGLWGVQAPVGDRSTVSSLLTPNSRLLLLLIAPFTDSGSVNRNSYLGHLLTLYREAIGQAQVDEQTFQEITSVSRALGQNDTDSLRATLNFLLTNRQQKIPAQYALSAEEERILRYVQQSVGLFLMQEGATPSAALDMTARNMEPSMYAANRPFINKLMDYLHRAAVMNTDYFTNAILNPHWLPPPGFYTGEYDMPDPNDGFLWDDVDSVVFSPTFQKRQEAPPSEGAVGRSPFPSLGSLHSLPGSVNSGRVSRPRLLGEDEYLNDSLLQPPRAKNAMANNGIESLVDKLNRWKTYAQDHRDAPAPRRQRHDRQRGLVWDDEDSADDSSVLDLGGSGGVNPFAHLQPKLGRRMF

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

Entity 5 polymer

description	Pre-hexon-linking protein VIII
formula_weight	24660.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,P

MSKEIPTPYMWSYQPQMGLAAGASQDYSTRMNWLSAGPSMISRVNGVRNHRNQILLEQAAVTSTPRAKLNPRNWPSTLVYQEIPGPTTVLLPRDALAEVRMTNSGVQLAGGASRCPLRPQSGIKTLVIRGRGTQLNDELVSSSIGLRPDGVFQLAGAGRSSFTPNQAYLTLQSSSSEPRSGGIGTLQFVEEFVPSVYFNPFSGSPGLYPDEFIPNFDAVREAVDGYD

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

Entity 6 polymer

description	Hexon-interlacing protein
formula_weight	13773.4 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	Q,R,S,T

MNGTGGAFEGGLFSPYLTTRLPGWAGVRQNVMGSTVDGRPVLPANSSTMTYATVGSSSLDSTAAAAAAAAAMTATRLASSYMPSSGSSPSVPSSIIAEEKLLALLAELEALSRQLAALTQQVSELREQQQQQNK

Source

organism	Human adenovirus D10
ncbi_taxonomy_id	28275
host_organism	Homo sapiens

▶

6. Citations (2)

▶

resolution	3.30 Å
resolution_method	—
num_particles	5524

fit	/app/data/saxs_computation/r7/9r78/9r78.fit
pddf	/app/data/pr_computation/r7/9r78/9r78.pr.out
profile	/app/data/saxs_computation/r7/9r78/9r78.dat

Human Adenovirus D 10 Capsid Structure

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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 (2)

7. Files & Curves (10)

Files (7)

Curves (3)