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- PDB-7cue: Crystal structure of HID2 bound to human Hemoglobin -

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Basic information

Entry
Database: PDB / ID: 7cue
TitleCrystal structure of HID2 bound to human Hemoglobin
Components
  • (Hemoglobin subunit ...) x 2
  • Amino acid ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Hemoglobin / Staphylococcus aureus / Hemoglobin binding protein / protein-protein interaction / Shr / heme acquisition
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Hemoglobin, pi / Hemoglobin, alpha-type ...Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Globin/Protoglobin / Leucine-rich repeat profile. / Leucine-rich repeat / Globin domain profile. / Globin / Globin / Leucine-rich repeat domain superfamily / Globin-like superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme-binding protein Shr / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsCaaveiro, J.M.M. / Hoshino, M. / Tsumoto, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K06962 Japan
CitationJournal: To Be Published
Title: Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes
Authors: Caaveiro, J.M.M. / Hoshino, M. / Senoo, A. / Nakakido, M. / Nagatoishi, S. / Tame, J.R.H. / Tsumoto, K.
History
DepositionAug 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Amino acid ABC transporter substrate-binding protein
F: Amino acid ABC transporter substrate-binding protein
H: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,37113
Polymers103,7137
Non-polymers2,6586
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-153 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.500, 52.760, 129.170
Angle α, β, γ (deg.)90.000, 118.350, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F
14E
24H
15F
25H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARGAA1 - 1412 - 142
21VALVALARGARGCC1 - 1412 - 142
12VALVALHISHISBB1 - 1462 - 147
22VALVALHISHISDD1 - 1462 - 147
13LEULEUGLNGLNEE176 - 2836 - 113
23LEULEUGLNGLNFF176 - 2836 - 113
14LEULEUGLNGLNEE176 - 2836 - 113
24LEULEUGLNGLNHG176 - 2836 - 113
15LEULEUGLNGLNFF176 - 2836 - 113
25LEULEUGLNGLNHG176 - 2836 - 113

NCS ensembles :
ID
1
2
3
4
5

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#1: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15281.550 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Human blood / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16021.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Human blood / References: UniProt: P68871

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Protein , 1 types, 3 molecules EFH

#3: Protein Amino acid ABC transporter substrate-binding protein / DUF1533 domain-containing protein / Heme-binding protein Shr


Mass: 13702.384 Da / Num. of mol.: 3 / Fragment: HID2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: shr, inlA_2, G3M98_06270, GTK50_07335, SAMEA3919037_01262
Production host: Escherichia coli (E. coli) / References: UniProt: B0LFQ8

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Non-polymers , 3 types, 28 molecules

#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% PEG 3350 (w/v), 100mM ammonium sulfate, 100mM BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→44.2 Å / Num. obs: 24514 / % possible obs: 87.9 % / Redundancy: 4.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.056 / Net I/σ(I): 8.7
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2 / Num. unique obs: 3018 / CC1/2: 0.749 / Rpim(I) all: 0.326

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CUD, 4NI0

7cud

4ni0


Resolution: 2.75→43.46 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.778 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1224 5 %RANDOM
Rwork0.2122 ---
obs0.2146 23276 87.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.15 Å2 / Biso mean: 62.79 Å2 / Biso min: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å21.15 Å2
2---1.45 Å20 Å2
3---1.53 Å2
Refinement stepCycle: final / Resolution: 2.75→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6889 0 182 22 7093
Biso mean--51.97 40.45 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176750
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.6779882
X-RAY DIFFRACTIONr_angle_other_deg1.191.60415655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08724.175297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.468151195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6321515
X-RAY DIFFRACTIONr_chiral_restr0.060.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028054
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021439
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41770.12
12C41770.12
21B43180.12
22D43180.12
31E30910.11
32F30910.11
41E30980.1
42H30980.1
51F31220.1
52H31220.1
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 79 -
Rwork0.35 1421 -
all-1500 -
obs--73.1 %

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