7CUE | pdb_00007cue

Crystal structure of HID2 bound to human Hemoglobin

• PDB DOI: https://doi.org/10.2210/pdb7CUE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens, Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-22 Released: 2021-07-07 
• Deposition Author(s): Caaveiro, J.M.M., Hoshino, M., Tsumoto, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Models: experimental

Literature

Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes

Caaveiro, J.M.M., Hoshino, M., Senoo, A., Nakakido, M., Nagatoishi, S., Tame, J.R.H., Tsumoto, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A4B3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 106.37 kDa 
• Atom Count: 7,093 
• Modeled Residue Count: 898 
• Deposited Residue Count: 950 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	142	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	147	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid ABC transporter substrate-binding protein	E, F, G [auth H]	124	Streptococcus pyogenes	Mutation(s): 0  Gene Names: shr, inlA_2, G3M98_06270, GTK50_07335, SAMEA3919037_01262
UniProt
Find proteins for Q99YA0 (Streptococcus pyogenes serotype M1) Explore Q99YA0  Go to UniProtKB:  Q99YA0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	H [auth A], I [auth B], K [auth C], L [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	J [auth B], M [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.5	α = 90
b = 52.76	β = 118.35
c = 129.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Caaveiro, J.M.M., Hoshino, M., Tsumoto, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15K06962

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description