8axk

Type 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Surface presentation of antigens protein SpaP

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAP_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216 Author chain C； PDBConstruct 1–216； UniProt 1–216 Author chain D； PDBConstruct 1–216； UniProt 1–216 Author chain E； PDBConstruct 1–216； UniProt 1–216

Surface presentation of antigens protein SpaR

OrganismNot specified

UniProt P0A1M6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAR_SHIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–256； UniProt 1–256

Surface presentation of antigens protein SpaQ

OrganismNot specified

UniProt P0A1M4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAQ_SHIFL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–86； UniProt 1–86 Author chain H； PDBConstruct 1–86； UniProt 1–86 Author chain I； PDBConstruct 1–86； UniProt 1–86 Author chain J； PDBConstruct 1–86； UniProt 1–86

Surface presentation of antigens protein SpaS

OrganismNot specified

UniProt P0A1M8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAS_SHIFL
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain K； PDBConstruct 1–342； UniProt 1–342

Protein MxiI

OrganismNot specified

UniProt P0A225

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MXII_SHIFL
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain M； PDBConstruct 1–97； UniProt 1–97 Author chain N； PDBConstruct 1–97； UniProt 1–97 Author chain O； PDBConstruct 1–97； UniProt 1–97 Author chain P； PDBConstruct 1–97； UniProt 1–97 Author chain Q； PDBConstruct 1–97； UniProt 1–97 Author chain R； PDBConstruct 1–97； UniProt 1–97

Protein MxiH

Shigella flexneri

UniProt P0A223

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Outer membrane protein MxiD × 16 （Q04641） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MXIH_SHIFL
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain S； PDBConstruct 16–98； UniProt 1–83 Author chain T； PDBConstruct 16–98； UniProt 1–83 Author chain U； PDBConstruct 16–98； UniProt 1–83 Author chain V； PDBConstruct 16–98； UniProt 1–83 Author chain W； PDBConstruct 16–98； UniProt 1–83 Author chain a； PDBConstruct 16–98； UniProt 1–83 Author chain b； PDBConstruct 16–98； UniProt 1–83 Author chain c； PDBConstruct 16–98； UniProt 1–83 Author chain d； PDBConstruct 16–98； UniProt 1–83 Author chain e； PDBConstruct 16–98； UniProt 1–83 Author chain f； PDBConstruct 16–98； UniProt 1–83 Author chain g； PDBConstruct 16–98； UniProt 1–83 Author chain h； PDBConstruct 16–98； UniProt 1–83 Author chain i； PDBConstruct 16–98； UniProt 1–83 Author chain j； PDBConstruct 16–98； UniProt 1–83 Author chain k； PDBConstruct 16–98； UniProt 1–83 Author chain l； PDBConstruct 16–98； UniProt 1–83 Author chain m； PDBConstruct 16–98； UniProt 1–83 Author chain n； PDBConstruct 16–98； UniProt 1–83 Author chain o； PDBConstruct 16–98； UniProt 1–83 Author chain p； PDBConstruct 16–98； UniProt 1–83 Author chain q； PDBConstruct 16–98； UniProt 1–83 Author chain r； PDBConstruct 16–98； UniProt 1–83 Author chain s； PDBConstruct 16–98； UniProt 1–83 Author chain t； PDBConstruct 16–98； UniProt 1–83 Author chain u； PDBConstruct 16–98； UniProt 1–83 Author chain v； PDBConstruct 16–98； UniProt 1–83 Author chain w； PDBConstruct 16–98； UniProt 1–83

Outer membrane protein MxiD

OrganismNot specified

UniProt Q04641

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Lipoprotein MxiJ × 24 （Q06081）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MXID_SHIFL
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain 0； PDBConstruct 1–566； UniProt 1–566 Author chain 1； PDBConstruct 1–566； UniProt 1–566 Author chain 2； PDBConstruct 1–566； UniProt 1–566 Author chain 3； PDBConstruct 1–566； UniProt 1–566 Author chain 4； PDBConstruct 1–566； UniProt 1–566 Author chain 5； PDBConstruct 1–566； UniProt 1–566 Author chain 6； PDBConstruct 1–566； UniProt 1–566 Author chain 7； PDBConstruct 1–566； UniProt 1–566 Author chain 8； PDBConstruct 1–566； UniProt 1–566 Author chain 9； PDBConstruct 1–566； UniProt 1–566 Author chain X； PDBConstruct 1–566； UniProt 1–566 Author chain Y； PDBConstruct 1–566； UniProt 1–566 Author chain Z； PDBConstruct 1–566； UniProt 1–566 Author chain x； PDBConstruct 1–566； UniProt 1–566 Author chain y； PDBConstruct 1–566； UniProt 1–566 Author chain z； PDBConstruct 1–566； UniProt 1–566

Lipoprotein MxiJ

OrganismNot specified

UniProt Q06081

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 85	Surface presentation of antigens protein SpaP × 5 （P0A1L3） Surface presentation of antigens protein SpaR × 1 （P0A1M6） Surface presentation of antigens protein SpaQ × 4 （P0A1M4） Surface presentation of antigens protein SpaS × 1 （P0A1M8） Protein MxiI × 6 （P0A225） Protein MxiH × 28 （P0A223） Outer membrane protein MxiD × 16 （Q04641）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MXIJ_SHIFL
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain a0； PDBConstruct 1–241； UniProt 1–241 Author chain b0； PDBConstruct 1–241； UniProt 1–241 Author chain c0； PDBConstruct 1–241； UniProt 1–241 Author chain d0； PDBConstruct 1–241； UniProt 1–241 Author chain e0； PDBConstruct 1–241； UniProt 1–241 Author chain f0； PDBConstruct 1–241； UniProt 1–241 Author chain g0； PDBConstruct 1–241； UniProt 1–241 Author chain h0； PDBConstruct 1–241； UniProt 1–241 Author chain i0； PDBConstruct 1–241； UniProt 1–241 Author chain j0； PDBConstruct 1–241； UniProt 1–241 Author chain k0； PDBConstruct 1–241； UniProt 1–241 Author chain l0； PDBConstruct 1–241； UniProt 1–241 Author chain m0； PDBConstruct 1–241； UniProt 1–241 Author chain n0； PDBConstruct 1–241； UniProt 1–241 Author chain o0； PDBConstruct 1–241； UniProt 1–241 Author chain p0； PDBConstruct 1–241； UniProt 1–241 Author chain q0； PDBConstruct 1–241； UniProt 1–241 Author chain r0； PDBConstruct 1–241； UniProt 1–241 Author chain s0； PDBConstruct 1–241； UniProt 1–241 Author chain t0； PDBConstruct 1–241； UniProt 1–241 Author chain u0； PDBConstruct 1–241； UniProt 1–241 Author chain v0； PDBConstruct 1–241； UniProt 1–241 Author chain w0； PDBConstruct 1–241； UniProt 1–241 Author chain x0； PDBConstruct 1–241； UniProt 1–241

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8axk
Deposition date deposition_date	2022-08-31
Structure title title	Type 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri
Keywords keywords	type 3 secretion, needle complex, virulence factor, shigella, infection, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8axk__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8axk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8axk__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	68.27 Å
Rg (electron density)	68.74 Å
Total Rg	68.63 Å
Atom count	44141
Residues	5608
Excluded volume	798850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8axk__assembly_1__model_1`	85-meric （85）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Surface presentation of antigens protein SpaP
Molecular weight formula_weight	24215.6 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	44141

MLSDMSLIATLSFFTLLPFLVAAGTCYIKFSIVFVMVRNALGLQQVPSNMTLNGIALIMALFVMKPIIEAGYENYLNGPQKFDTISDIVRFSDSGLMEYKQYLKKHTDLELARFFQRSEEENADLKSAENNDYSLFSLLPAYALSEIKDAFKIGFYLYLPFVVVDLVISSILLALGMMMMSPITISVPIKLVLFVALDGWGILSKALIEQYINIPA

Entity 2 Entity 2 polymer

Description description	Surface presentation of antigens protein SpaR
Molecular weight formula_weight	28513.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MDISSWFESIHVFLILLNGVFFRLAPLFFFLPFLNNGIISPSIRIPVIFLVASGLITSGKVDIGSSVFEHVYFLMFKEIIVGLLLSFCLSLPFWIFHAVGSIIDNQRGATLSSSIDPANGVDTSELAKFFNLFSAVVFLYSGGMVFILESIQLSYNICPLFSQCSFRISNILTFLTLLASQAVILASPVMIVLLLSEVLLGVLSRFAPQMNAFSVSLTIKSLLAIFIIFICSSTIYFSKVQFFLGEHKFFTNLFVR

Entity 3 Entity 3 polymer

Description description	Surface presentation of antigens protein SpaQ
Molecular weight formula_weight	9433.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J

MSDIVYMGNKALYLILIFSLWPVGIATVIGLSIGLLQTVTQLQEQTLPFGIKLIGVSISLLLLSGWYGEVLLSFCHEIMFLIKSGV

Entity 4 Entity 4 polymer

Description description	Surface presentation of antigens protein SpaS
Molecular weight formula_weight	39903.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MANKTEKPTPKKLKDAAKKGQSFKFKDLTTVVIILVGTFTIISFFSLSDVMLLYRYVIINDFEINEGKYFFAVVIVFFKIIGFPLFFCVLSAVLPTLVQTKFVLATKAIKIDFSVLNPVKGLKKIFSIKTIKEFFKSILLLIILALTTYFFWINDRKIIFSQVFSSVDGLYLIWGRLFKDIILFFLAFSILVIILDFVIEFILYMKDMMMDKQEIKREYIEQEGHFETKSRRRELHIEILSEQTKSDIRNSKLVVMNPTHIAIGIYFNPEIAPAPFISLIETNQCALAVRKYANEVGIPTVRDVKLARKLYKTHTKYSFVDFEHLDEVLRLIVWLEQVENTH

Entity 5 Entity 5 polymer

Description description	Protein MxiI
Molecular weight formula_weight	10640.0 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R

MNYIYPVNQVDIIKASDFQSQEISSLEDVVSAKYSDIKMDTDIQVSQIMEMVSNPESLNPESLAKLQTTLSNYSIGVSLAGTLARKTVSAVETLLKS

Entity 6 Entity 6 polymer

Description description	Protein MxiH
Molecular weight formula_weight	11060.3 kDa
Source method src_method	man
Copy count entity_count	28

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T,U,V,W,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w

MASWSHPQFEKIEGRMSVTVPNDDWTLSSLSETFDDGTQTLQGELTLALDKLAKNPSNPQLLAEYQSKLSEYTLYRNAQSNTVKVIKDVDAAIIQNFR

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Shigella flexneri

Entity 7 Entity 7 polymer

Description description	Outer membrane protein MxiD
Molecular weight formula_weight	63230.4 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y,Z,0,2,4,6,8,x,y,z,1,3,5,7,9

MKKFNIKSLTLLIVLLPLIVNANNIDSHLLEQNDIAKYVAQSDTVGSFFERFSALLNYPIVVSKQAAKKRISGEFDLSNPEEMLEKLTLLVGLIWYKDGNALYIYDSGELISKVILLENISLNYLIQYLKDANLYDHRYPIRGNISDKTFYISGPPALVELVANTATLLDKQVSSIGTDKVNFGVIKLKNTFVSDRTYNMRGEDIVIPGVATVVERLLNNGKALSNRQAQNDPMPPFNITQKVSEDSNDFSFSSVTNSSILEDVSLIAYPETNSILVKGNDQQIQIIRDIITQLDVAKRHIELSLWIIDIDKSELNNLGVNWQGTASFGDSFGASFNMSSSASISTLDGNKFIASVMALNQKKKANVVSRPVILTQENIPAIFDNNRTFYVSLVGERNSSLEHVTYGTLINVIPRFSSRGQIEMSLTIEDGTGNSQSNYNYNNENTSVLPEVGRTKISTIARVPQGKSLLIGGYTHETNSNEIISIPFLSSIPVIGNVFKYKTSNISNIVRVFLIQPREIKESSYYNTAEYKSLISEREIQKTTQIIPSETTLLEDEKSLVSYLNY

Entity 8 Entity 8 polymer

Description description	Lipoprotein MxiJ
Molecular weight formula_weight	27542.1 kDa
Source method src_method	nat
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a0,b0,c0,d0,e0,f0,g0,h0,i0,j0,k0,l0,m0,n0,o0,p0,q0,r0,s0,t0,u0,v0,w0,x0

MIRYKGFILFLLLMLIGCEQREELISNLSQRQANEIISVLERHNITARKVDGGKQGISVQVEKGTFASAVDLMRMYDLPNPERVDISQMFPTDSLVSSPRAEKARLYSAIEQRLEQSLVSIGGVISAKIHVSYDLEEKNISSKPMHISVIAIYDSPKESELLVSNIKRFLKNTFSDVKYENISVILTPKEEYVYTNVQPVKEVKSEFLTNEVIYLFLGMAVLVVILLVWAFKTGWFKRNKI

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.05 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	90547

Type 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri

1. Protein Identity and Related Structures Protein Identity & Related Structures

Surface presentation of antigens protein SpaP

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Surface presentation of antigens protein SpaR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Surface presentation of antigens protein SpaQ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Surface presentation of antigens protein SpaS

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein MxiI

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein MxiH

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Outer membrane protein MxiD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lipoprotein MxiJ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8axk__assembly_1__model_1

8axk__assembly_1__model_1 | I(q)

8axk__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer