SAXSdb — 8hc1

▼

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

Urease subunit alpha

Helicobacter pylori 26695

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	Urease subunit beta × 12 （P69996） Urease accessory protein UreH × 12 （Q09067） Urease accessory protein UreF × 12 （Q09065）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE23_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–238； UniProt 1–238 Author chain E； PDBConstruct 1–238； UniProt 1–238 Author chain I； PDBConstruct 1–238； UniProt 1–238 Author chain M； PDBConstruct 1–238； UniProt 1–238 Author chain Q； PDBConstruct 1–238； UniProt 1–238 Author chain U； PDBConstruct 1–238； UniProt 1–238 Author chain Y； PDBConstruct 1–238； UniProt 1–238 Author chain c； PDBConstruct 1–238； UniProt 1–238 Author chain g； PDBConstruct 1–238； UniProt 1–238 Author chain k； PDBConstruct 1–238； UniProt 1–238 Author chain o； PDBConstruct 1–238； UniProt 1–238 Author chain s； PDBConstruct 1–238； UniProt 1–238

Urease subunit beta

Helicobacter pylori 26695

UniProt P69996

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	Urease subunit alpha × 12 （P14916） Urease accessory protein UreH × 12 （Q09067） Urease accessory protein UreF × 12 （Q09065）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE1_HELPY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–569； UniProt 1–569 Author chain F； PDBConstruct 1–569； UniProt 1–569 Author chain J； PDBConstruct 1–569； UniProt 1–569 Author chain N； PDBConstruct 1–569； UniProt 1–569 Author chain R； PDBConstruct 1–569； UniProt 1–569 Author chain V； PDBConstruct 1–569； UniProt 1–569 Author chain Z； PDBConstruct 1–569； UniProt 1–569 Author chain d； PDBConstruct 1–569； UniProt 1–569 Author chain h； PDBConstruct 1–569； UniProt 1–569 Author chain l； PDBConstruct 1–569； UniProt 1–569 Author chain p； PDBConstruct 1–569； UniProt 1–569 Author chain t； PDBConstruct 1–569； UniProt 1–569

Urease accessory protein UreH

Helicobacter pylori 26695

UniProt Q09067

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	Urease subunit alpha × 12 （P14916） Urease subunit beta × 12 （P69996） Urease accessory protein UreF × 12 （Q09065）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UREH_HELPY
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–265； UniProt 1–265 Author chain G； PDBConstruct 1–265； UniProt 1–265 Author chain K； PDBConstruct 1–265； UniProt 1–265 Author chain O； PDBConstruct 1–265； UniProt 1–265 Author chain S； PDBConstruct 1–265； UniProt 1–265 Author chain W； PDBConstruct 1–265； UniProt 1–265 Author chain a； PDBConstruct 1–265； UniProt 1–265 Author chain e； PDBConstruct 1–265； UniProt 1–265 Author chain i； PDBConstruct 1–265； UniProt 1–265 Author chain m； PDBConstruct 1–265； UniProt 1–265 Author chain q； PDBConstruct 1–265； UniProt 1–265 Author chain u； PDBConstruct 1–265； UniProt 1–265

Urease accessory protein UreF

Helicobacter pylori 26695

UniProt Q09065

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 48	Urease subunit alpha × 12 （P14916） Urease subunit beta × 12 （P69996） Urease accessory protein UreH × 12 （Q09067）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UREF_HELPY
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–254； UniProt 1–254 Author chain H； PDBConstruct 1–254； UniProt 1–254 Author chain L； PDBConstruct 1–254； UniProt 1–254 Author chain P； PDBConstruct 1–254； UniProt 1–254 Author chain T； PDBConstruct 1–254； UniProt 1–254 Author chain X； PDBConstruct 1–254； UniProt 1–254 Author chain b； PDBConstruct 1–254； UniProt 1–254 Author chain f； PDBConstruct 1–254； UniProt 1–254 Author chain j； PDBConstruct 1–254； UniProt 1–254 Author chain n； PDBConstruct 1–254； UniProt 1–254 Author chain r； PDBConstruct 1–254； UniProt 1–254 Author chain v； PDBConstruct 1–254； UniProt 1–254

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8hc1
Deposition date deposition_date	2022-11-01
Structure title title	CryoEM structure of Helicobacter pylori UreFD/urease complex
Keywords keywords	Urease, activation complex, UreA, UreB, UreC, UreF, UreD, UreH, Helicobacter pylori, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8hc1__assembly_1__model_1

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

Download this curve (.dat)

8hc1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8hc1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	79.30 Å
Rg (electron density)	79.25 Å
Total Rg	79.42 Å
Atom count	119844
Residues	15468
Excluded volume	2136100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8hc1__assembly_1__model_1`	48-meric （48）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Urease subunit alpha
Molecular weight formula_weight	26587.7 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M,Q,U,Y,c,g,k,o,s
Atom count atom_count	120048

MKLTPKELDKLMLHYAGELAKKRKEKGIKLNYVEAVALISAHIMEEARAGKKTAAELMQEGRTLLKPDDVMDGVASMIHEVGIEAMFPDGTKLVTVHTPIEANGKLVPGELFLKNEDITINEGKKAVSVKVKNVGDRPVQIGSHFHFFEVNRCLDFDREKTFGKRLDIASGTAVRFEPGEEKSVELIDIGGNRRIFGFNALVDRQADNESKKIALHRAKERGFHGAKSDDNYVKTIKE

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Urease subunit beta
Molecular weight formula_weight	61759.5 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N,R,V,Z,d,h,l,p,t

MKKISRKEYVSMYGPTTGDKVRLGDTDLIAEVEHDYTIYGEELKFGGGKTLREGMSQSNNPSKEELDLIITNALIVDYTGIYKADIGIKDGKIAGIGKGGNKDMQDGVKNNLSVGPATEALAGEGLIVTAGGIDTHIHFISPQQIPTAFASGVTTMIGGGTGPADGTNATTITPGRRNLKWMLRAAEEYSMNLGFLAKGNASNDASLADQIEAGAIGFKIHEDWGTTPSAINHALDVADKYDVQVAIHTDTLNEAGCVEDTMAAIAGRTMHTFHTEGAGGGHAPDIIKVAGEHNILPASTNPTIPFTVNTEAEHMDMLMVCHHLDKSIKEDVQFADSRIRPQTIAAEDTLHDMGIFSITSSDSQAMGRVGEVITRTWQTADKNKKEFGRLKEEKGDNDNFRIKRYLSKYTINPAIAHGISEYVGSVEVGKVADLVLWSPAFFGVKPNMIIKGGFIALSQMGDANASIPTPQPVYYREMFAHHGKAKYDANITFVSQAAYDKGIKEELGLERQVLPVKNCRNITKKDMQFNDTTAHIEVNPETYHVFVDGKEVTSKPANKVSLAQLFSIF

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Urease accessory protein UreH
Molecular weight formula_weight	30741.2 kDa
Mutation mutation	E140A
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O,S,W,a,e,i,m,q,u

MNTYAQESKLRLKTKIGADGRCVIEDNFFTPPFKLMAPFYPKDDLAEIMLLAVSPGMMRGDAQDVQLNIGPNCKLRITSQSFEKIHNTEDGFASRDMHIVVGENAFLDFAPFPLIPFENAHFKGNTTISLRSSSQLLYSAIIVAGRVARNELFKFNRLHTKISILQDEKPIYYDNTILDPKTTDLNNMCMFDGYTHYLNLVLVNCPIELSGVRECIEESEGVDGAVSETASSHLCVKALAKGSEPLLHLREKIARLVTQTTTQKVWSHPQFEK

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Urease accessory protein UreF
Molecular weight formula_weight	28517.6 kDa
Mutation mutation	R179A, Y183D
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P,T,X,b,f,j,n,r,v

MDKGKSVKSTEKSVGMPPKTPKTDNNAHVDNEFLILQVNDAVFPIGSYTHSFGLETYIQQKKVTNKESALEYLKANLSSQFLYTEMLSLKLTYESALQQDLKKILGVEEVIMLSTSPMELRLANQKLGNRFIKTLQAMNELDMGEFFNAYAQKTKDPTHATSYGVFAASLGIELKKALAHYLDAQTSNMVINCVKSVPLSQNDGQKILLSLQSPFNQLIEKTLELDESHLCTASVQNDIKAMQHESLYSRLYMS

Source Source

Source organism organism	Helicobacter pylori 26695
NCBI taxonomy ID ncbi_taxonomy_id	85962
Host organism host_organism	Escherichia coli

▶

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	2.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	68516

CryoEM structure of Helicobacter pylori UreFD/urease complex

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

Urease subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Urease subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Urease accessory protein UreH

State in the Current Structure

Other States of the Same Protein in the Database

Urease accessory protein UreF

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8hc1__assembly_1__model_1

8hc1__assembly_1__model_1 | I(q)

8hc1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)

CryoEM structure of Helicobacter pylori UreFD/urease complex

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

Urease subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urease subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urease accessory protein UreH

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urease accessory protein UreF

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

8hc1__assembly_1__model_1

8hc1__assembly_1__model_1 | I(q)

8hc1__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

7. Citations (1)