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9qgl

Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state

Method: ELECTRON MICROSCOPY D_max: 269.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qgl
deposition_date	2025-03-14
title	Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state
keywords	Contractile injection system, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	— Å
rg_electron	101.50 Å
i0	77907900000.00
molecular_weight	2422200.0 kDa
excluded_volume	3041300 Å³
envelope_volume	5535500 Å³
shell_volume	438330 Å³
envelope_diameter	343.2 Å
shell_rg	110.20 Å
envelope_rg	96.78 Å
shape_rg	101.50 Å
total_rg	101.60 Å
total_atoms	171084
n_residues	21576
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	269.1 Å
rg_real	98.94 Å
rg_real_error	0.58 Å
i0_real	7.4470e+10
i0_real_error	1.3950e+09
rg_reciprocal	104.20 Å
i0_reciprocal	78440000000.0000
total_estimate	0.9065
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	125.6 Å
skewness	0.109
kurtosis	-0.500
angular_range	— – 0.0750 Å⁻¹
current_alpha	1.0170
highest_alpha	5340000000.0000
n_real_points	16
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.997; Stabil: 0.956; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Phage tail protein
formula_weight	16574.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	1A,1B,1C,1D,1E,1F
atom_count	171084

MAITPEQIAVEYPIPTYRFVVSVGDEQIPFNNVSGLDVHYDVIEYKDGIGNYYKMPGQRQSINITLRKGVFPGDTKLFDWINSIQLNQVEKKDIAISLTNEAGTEILMTWNVANAFPTSFTSPSFDATSNEIAVQEIALTADRVTIQAA

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 2 polymer

description	Phage tail sheath family protein
formula_weight	39009.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	2A,2B,2C,2D,2E,2F

MTTITTYPGVYIEEDASLSLSVSSSATAVPVFAVAGDNPLISGKPYIRISNWLEYLTLKNEQFDPANTLDISLRAYFINGGGYCYLVQTTDLEKQVPKLDDVTLLVAAGENITTAVSTLCKPGKGLFAIFDGPTTELKSDGTSNSDYDPNPFAAVYYPWLTADWTTTIDIPPSAAIAGVYCSVDSTRGVWKAPANVPIQGGLQPKYPVTDDLQAQYNQGKALNMIRTFPKSGTLVWGARTLEDNDNWRYIPVRRLFNSAERDIKNAMSFAVFEPNSQPTWERVRSAVNNYLYSLWQQGGLAGNKPDDAYFVQIGKDITMTDDDIKQGKMIIKIGMAAVRPAEFIILQFTQNTAQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 3 polymer

description	Phage tail protein
formula_weight	17178.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	5A,5B,5C,5D,5E,5F

MHNLYTPSVSHRFIASFLFNNIPSPLDIAFQRISGLSRELQTTQYSQGGENARNVWLAEKIQHGSLHLERGVMTVTPLTLMFDRVLRGEKAVYADVVIMLLNENSVPVASWTLSNALPVRWSTGDFDANSNAVLVNSLELRYQDMRWLGVKV

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 4 polymer

description	Contractile injection system tube protein N-terminal domain-containing protein
formula_weight	24840.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	7A,7B,7C,7D,7E,7F

MSLIERGLSKLTLTAFKDREGKISVGSLQAMYNPDAIQLDYQTHYQQDESVNHTRKSSHYVSSPPAGLSLVLLFDASMPGNNIPVETQLTTLKALCAVDPSTHVPHFLKIKWGKMRWENKSYFAGRASGLTINYTLFDRDATPLRASATLSLVADESFVIQATEQQLKSPPVTTVSVTDMLTLPLIALGAGASLASGIDYLSLAWQNDLDNLDDFTPGQTLQAQEKA

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 5 polymer

description	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
formula_weight	27145.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	9A,9B,9C,9D,9E,9F

MTNKILADIYGRGWAFPPQFFIGERIPYEDYSSDLNKYLSEKKIEAEQIVKIQACIKESVMCYDFHAKITSTQVSKQTNLPNPLNILVTYTLGDSEISQKIQGVLRVSQDDPPQFSIKDNSRTGIAIAEGTQNVLQSINILFLTEPGERIMREDYGCGLNDYLFANISDELMTDIQTHIEERVLRYEPRAEITSIQVNQRTNLPSTLHVQVTYALRGSDINQQIEGVLEVNEGRVQVSL

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 6 polymer

description	Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
formula_weight	101454.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F

MGQAELDNKLSAIVPDTVFKLDERSTLDILNWLKAYAEKIPFDQDKNQFWDSFYFIQENTPEELEDIYQHANKADGLLPPHQAFVFAFLKLLETSNRLLNTFPARHRDLYYRELLGLSPRKAQADSVALGITLNTDNAEYLIPKGTLFDAGQDSVGNPLQYTSETDLLANQGELTDLRWYRKDKDSWQSTIPLSLSDNIALPENGIQLFSPTANDVAVLSGYLIKSSLFSMPEGERHITLTLENDWEGQAEHLTAKISTGDHWLSLSVNPNRTNKNTIELELSSTDDPISPPDNLDGMTFDIPVLKLGTTQKPMLPKITGIEININGNRSVRYASDGGIEQTDTTSSPFGQSPSLGSGFNLVAPEWYGTENATLTMTPQWVGLPTSSFSTWYDKYNPKPASNGVFKVQGYLVTSQKRDVLNDAKSQPLFDGTGAPQGQSLTFILPAMHYPLTDSPSPNEWPASVRIELAEQDFMHAQYWQNPTDKNVPYTPQISALQIQFSTTAKPEQFTVYPLTPFGWANTNEDPPSFTNDALYLGFTNVLPGQTLSLYWQLEGFKALNLSWFYLNQSNTWGSLDQLVDDQTHNLFDQGTWRTLLPQDASNQATLMPTGRYWLKAEITHQAESQDYPKIKGILYNAATATLINAELVETDHFINGLPADSITQPVNALVAIDSINQPWVSWNGRPEETEQAFLTRVSARLSHRNRVLSWDNIVTLLKEQFVSLFDVKYPSASELTKIPAQKEQQLIAIPDSRYKDNDDALRPILNPARLAEMVDWISQLSSPWTTLKINNPTYVDVLISYQLVFVTGINPDYGRHQLQQELSRKYMPWAEDSAIGVTTGNRIDYYPLLATIQQSPLVERVTNLTLKKSSQTAGAVGDSVEAADNEVLILVWSENSSTNKGADSE

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 7 polymer

description	Baseplate protein J-like domain-containing protein
formula_weight	110905.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e,f

MNNQDALFPIVKDDIAFETLLTQAKTVIEQQSGQLWSNTEENDPGITLLEACCYGASDLAYRHSLPLRDLLTPEKQEQTLGDGIFPQEFGPQQMLTCGPITAEDYRRALLDLHSSDTDNETSEDYFFFNDVRLICEPESERYKYWYNKESREYSFIQEQEQEQEQLQLTLRGNYWLYLLPNRETEDDKTLTQKRLNDFLKDNRNLGESVSKIIWLQPVDFLLQLDIELDDDVSDLADIFAQVYMTTEQMVLTSPLRYSTQAMIEQGYSNEEIFEGPYLHHGWIPELSAAKDYTKPTELKLSHLANRLLAIPGVQNITRLALGKHDENISPLADDSWSWTIAQGYYPRLWGNDPLDLISSSASPLTITAKGGVKITVSKQDIENKIIAEPLIETQPELLNWGKHRKVLDYYPVSNKLPACYGLQTYAETQQQVHLHQFMLPFEQMLANGCAELALLPKLLAFKQRGNTVYGTQWPFKANTVGQQVHQEIMPDLIKQLNNDSQINSDDGIHSQNYTKELSILNYLLEYFGTHRAARPLTLDSLDFLSTQRGYLAQQPELTYQRNNIRIDKVSALQKRIAARLGLGGKCFEETSKLDELPFYLIEHRQLLPVKPDTKFDKEQKPDKLKIKSVPNSKNQQLIITQNGTTGQLLYGQVINLIIKEKENQDIRVKFILRGQMITDITGESFILDTRNSTALARSLIDVQNAYNDGNLYWCNSPVWMEDMDYQLVYASEIYQTGTENERWITSSPQSPFPAMIEENDEITLKYVITPSGPKKSDHELKANVIKFDRIQGKILIKLTQDSQDNFPLAADAWRYRWYFSSEKYALADRFSFVVSMVINSQLVKNDDVDPYKLESWAKTEILAEFPAHLSMIIHWLSPEDFKDFVSTYQRWQNNGAPLGDEAYHVLETLTLGRLPSAATGIGNMRIATAQQRIGVVGESGKEWNTEVIISNQLVYVPYTGENLNKR

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 8 polymer

description	Phage tail sheath family protein
formula_weight	51330.9 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	3A,3B,3C,3D,3E,3F

MPTIPTYPGVYIEEDASLNLSVNQGNTAIPVFIGLFSPKNTNLKSQVTRVNSWLDFTNLFNAGCIAPITIKSTKRASMPAPTLLENVKGDTAVVATPGISVDADNKDPTYTYKVIVNYTTSSDALKLYFQNGGGPCYILPQLDRLTQGFLDSIPELIKQALEITLIVCPEWDSGYQSKIYNSLTSSLLNAGYFLIADNQDKNTALITEVASQTATYYPAVKVSQLIQAEDSQIAVSGYEDAKTKSDEVKNLAQLKEKNPTVYQQAVQKIQAIQDEIAANGNIIPVSAVMAGIYCATDASRGVWKAPANIVLSGISDVAERLTDDEQGEMNSKGINAIRYFSHKGFVVWGARTLQNDDNWRYIPVRRLFNAAERDIKQAMQSVVFEPNSQPTWERVKSAIDNYLYSLWQQGALAGNKPQEAYFVQIGKDVTMSDDDIKQGKMIVKVGMAAVRPAEFIILQFSQQVAQ

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 9 polymer

description	Phage tail sheath family protein
formula_weight	44076.1 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	4A,4B,4C,4D,4E,4F

MEITQPSVTITENLIFPKQNDSFIGIPVFIGYTSSPVDKTAIKLHSLADFARSFPESGLMYYSVRHFFENGGQQAYVLSLGTEQQLSDFSSLITALQQAWLAQTIAAENDITLIITPDVIRFDQTEISDTQRDLWLQLWQSVLNLCKSRRGIMGLLDAPDDPTLAAKCLQQFSSADRQWGVVYWPLLKSAYQDNTQNPIVLSPTAAVAAVIQRNDNQQGVWTAPANIALSKVISPVRAYIEANALFNPDGTSLNLVRSFPGKGIRIWGCRTLENTHDSPWSYIQTRRLVSYIEAYMTQLGRAFVFEPNNAITWMKFKGQAHNWLRQLWLKGGLRGTQEDQAFEVLLGVDESMREADLRAGKMIIKIRLAVLIPAEFIELNLTFDTRTGTIPS

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

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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	2.68 Å
resolution_method	—
num_particles	53537

fit	/app/data/saxs_computation/qg/9qgl/9qgl.fit
pddf	/app/data/pr_computation/qg/9qgl/9qgl.pr.out
profile	/app/data/saxs_computation/qg/9qgl/9qgl.dat

Cryo-EM structure of the PlPVC1 baseplate, 6-fold symmetrized (C6), in extended state

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 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)