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- PDB-8vyl: The structure of Human Hemoglobin in Complex with Nanobody BtNbE11 -

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Basic information

Entry
Database: PDB / ID: 8vyl
TitleThe structure of Human Hemoglobin in Complex with Nanobody BtNbE11
Components
  • (Hemoglobin subunit ...) x 2
  • Nanobody BtNbE11
KeywordsOXYGEN TRANSPORT / Hemoglobin / Nanobody
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
ACETYL GROUP / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsGrinter, R. / Binks, S. / Fox, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1197376 Australia
CitationJournal: Febs Lett. / Year: 2024
Title: The structure of a haemoglobin-nanobody complex reveals human beta-subunit-specific interactions.
Authors: Fox, D.R. / Samuels, I. / Binks, S. / Grinter, R.
History
DepositionFeb 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
C: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
D: Hemoglobin subunit beta
F: Nanobody BtNbE11
E: Nanobody BtNbE11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,20511
Polymers92,6956
Non-polymers2,5105
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.761, 74.837, 57.875
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number5
Space group name H-MC121

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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) / 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) / References: UniProt: P68871

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Antibody , 1 types, 2 molecules FE

#3: Antibody Nanobody BtNbE11


Mass: 15044.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Lama glama (llama)

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Non-polymers , 3 types, 445 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.41 % / Description: Flat plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1-0.3M NH4 Acet. pH 5.5, 0.1-0.3M Na Acet., 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 19, 2023 / Details: Yes
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→49.89 Å / Num. obs: 52426 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.072 / Net I/σ(I): 8.3
Reflection shellResolution: 2.02→2.08 Å / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1 / Num. unique obs: 3697 / CC1/2: 0.545 / Rpim(I) all: 0.775

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.89 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 2698 5.15 %
Rwork0.208 --
obs0.2108 52415 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 0 440 6839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056583
X-RAY DIFFRACTIONf_angle_d0.7239004
X-RAY DIFFRACTIONf_dihedral_angle_d10.684895
X-RAY DIFFRACTIONf_chiral_restr0.042975
X-RAY DIFFRACTIONf_plane_restr0.0061137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.060.32851380.2812433X-RAY DIFFRACTION93
2.06-2.10.33581500.27172589X-RAY DIFFRACTION100
2.1-2.140.33221300.26322668X-RAY DIFFRACTION100
2.14-2.190.28121630.24282562X-RAY DIFFRACTION100
2.19-2.240.30491300.23582596X-RAY DIFFRACTION100
2.24-2.30.28061380.22852624X-RAY DIFFRACTION100
2.3-2.360.28571360.23252658X-RAY DIFFRACTION100
2.36-2.430.29691440.22592576X-RAY DIFFRACTION100
2.43-2.510.30461440.22882633X-RAY DIFFRACTION100
2.51-2.60.27041410.24082585X-RAY DIFFRACTION100
2.6-2.70.32921230.2422646X-RAY DIFFRACTION100
2.7-2.820.32141530.22932610X-RAY DIFFRACTION100
2.82-2.970.25351570.22312617X-RAY DIFFRACTION100
2.97-3.160.28491710.22462593X-RAY DIFFRACTION100
3.16-3.40.27641450.22212653X-RAY DIFFRACTION100
3.4-3.740.23641290.1912638X-RAY DIFFRACTION100
3.75-4.290.25421290.17452654X-RAY DIFFRACTION100
4.29-5.40.23341170.17722683X-RAY DIFFRACTION100
5.4-49.890.19881600.16892699X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.7926 Å / Origin y: -24.4751 Å / Origin z: 3.8418 Å
111213212223313233
T0.2069 Å20.0275 Å20.0053 Å2-0.2319 Å20.0151 Å2--0.2748 Å2
L0.8071 °2-0.3495 °2-0.0163 °2-0.8304 °2-0.1927 °2--0.4821 °2
S0.0478 Å °0.1371 Å °0.3128 Å °-0.0977 Å °-0.0808 Å °-0.2481 Å °-0.0704 Å °0.026 Å °0.0242 Å °
Refinement TLS groupSelection details: all

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