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9rbq

Semliki Forest virus trimer 1 in complex with ApoER2 LA5

Method: ELECTRON MICROSCOPY D_max: 191.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rbq
deposition_date	2025-05-27
title	Semliki Forest virus trimer 1 in complex with ApoER2 LA5
keywords	Semliki Forest virus, SFV, ApoER2 receptor, localized reconstruction, VIRUS; VIRUS
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	61.34 Å
rg_electron	60.90 Å
i0	1964590000.00
molecular_weight	364950.0 kDa
excluded_volume	453440 Å³
envelope_volume	755090 Å³
shell_volume	103890 Å³
envelope_diameter	190.5 Å
shell_rg	63.34 Å
envelope_rg	58.79 Å
shape_rg	60.81 Å
total_rg	61.25 Å
total_atoms	25585
n_residues	3267
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	191.7 Å
rg_real	61.28 Å
rg_real_error	1.87 Å
i0_real	1.9650e+09
i0_real_error	4.0710e+07
rg_reciprocal	61.35 Å
i0_reciprocal	1965000000.0000
total_estimate	0.6150
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	66.3 Å
skewness	0.212
kurtosis	-0.613
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	76310000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	LDL receptor related protein 8,Ig gamma-2A chain C region, A allele
formula_weight	33306.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	25585

GSADPACGPREFRCGGDGGGACIPERWVCDRQFDCEDRSDEAAELCGRPGPGATSAPAAGSLEVLFQGPPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKDVLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTLRVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVYVLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGKTELNYKNTEPVLDSDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSRTPGK

Source

organism	Mus musculus
common_name	Mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	Protein E3
formula_weight	7384.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

SAPLITAMCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCRNGTRHRR

Source

organism	Semliki Forest virus
ncbi_taxonomy_id	11033
host_organism	Mesocricetus auratus

Entity 3 polymer

description	Structural polyprotein
formula_weight	47489.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I

YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR

Source

organism	Semliki Forest virus
ncbi_taxonomy_id	11033
host_organism	Mesocricetus auratus

Entity 4 polymer

description	Envelope glycoprotein E2
formula_weight	46870.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	J,K,L

SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Source

organism	Semliki Forest virus
ncbi_taxonomy_id	11033
host_organism	Mesocricetus auratus

Entity 5 polymer

description	Capsid protein
formula_weight	29920.7 kDa
ec_number	3.4.21.90
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	M,N,O

MNYIPTQTFYGRRWRPRPAARPWPLQATPVAPVVPDFQAQQMQQLISAVNALTMRQNAIAPARPPKPKKKKTTKPKPKTQPKKINGKTQQQKKKDKQADKKKKKPGKRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Source

organism	Semliki Forest virus
ncbi_taxonomy_id	11033
host_organism	Mesocricetus auratus

Entity 6 branched

description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	3

Entity 7 branched

description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	627.6 kDa
src_method	man
entity_count	3

Entity 8 branched

description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	830.8 kDa
src_method	man
entity_count	3

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

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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	2.70 Å
resolution_method	—
num_particles	2344552

fit	/app/data/saxs_computation/rb/9rbq/9rbq.fit
pddf	/app/data/pr_computation/rb/9rbq/9rbq.pr.out
profile	/app/data/saxs_computation/rb/9rbq/9rbq.dat

Semliki Forest virus trimer 1 in complex with ApoER2 LA5

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 (9)

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 branched

Entity 7 branched

Entity 8 branched

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)