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- PDB-9c18: Human biliverdin IX beta reductase in complex with NADP in space ... -

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Basic information

Entry
Database: PDB / ID: 9c18
TitleHuman biliverdin IX beta reductase in complex with NADP in space group P1
ComponentsFlavin reductase (NADPH)
KeywordsOXIDOREDUCTASE / NADP binding / heme degradation / thrombopoiesis
Function / homology
Function and homology information


FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation ...FMN reductase (NADH) activity / biliverdin reductase [NAD(P)H] activity / flavin reductase (NADPH) / FMN reductase (NADPH) activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / megakaryocyte differentiation / riboflavin reductase (NADPH) activity / heme catabolic process / Heme degradation / peptidyl-cysteine S-nitrosylase activity / negative regulation of insulin receptor signaling pathway / Cytoprotection by HMOX1 / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKreitler, D.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL150927 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL153144 United States
CitationJournal: Nat Commun / Year: 2025
Title: Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo.
Authors: Nesbitt, N.M. / Araldi, G.L. / Pennacchia, L. / Marchenko, N. / Assar, Z. / Muzzarelli, K.M. / Thekke Veedu, R.R. / Medel-Lacruz, B. / Lee, E. / Eisenmesser, E.Z. / Kreitler, D.F. / Bahou, W.F.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin reductase (NADPH)
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5884
Polymers45,1022
Non-polymers1,4872
Water3,207178
1
A: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2942
Polymers22,5511
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavin reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2942
Polymers22,5511
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.940, 41.977, 60.212
Angle α, β, γ (deg.)84.110, 87.240, 63.660
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Flavin reductase (NADPH) / FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / ...FR / Biliverdin reductase B / BVR-B / Biliverdin-IX beta-reductase / Green heme-binding protein / GHBP / NADPH-dependent diaphorase / NADPH-flavin reductase / FLR / S-nitroso-CoA-assisted nitrosyltransferase / SNO-CoA-assisted nitrosyltransferase


Mass: 22550.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLVRB, FLR, SCAN / Plasmid: pGEX / Details (production host): GST / Production host: Escherichia coli (E. coli)
References: UniProt: P30043, flavin reductase (NADPH), Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, Transferases; Transferring nitrogenous groups; ...References: UniProt: P30043, flavin reductase (NADPH), Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 12% (w/v) PEG20000, 25% (v/v) MPD, 1 mM NADP+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 2, 2024 / Details: KB bimorph
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.9→31.88 Å / Num. obs: 28264 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.12 / Rrim(I) all: 0.231 / Net I/σ(I): 4.3
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.996 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1414 / CC1/2: 0.367 / Rpim(I) all: 1.196 / Rrim(I) all: 2.33

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9C16

9c16


Resolution: 1.9→31.88 Å / SU ML: 0.2694 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.9649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 1640 5.84 %
Rwork0.2056 26444 -
obs0.2071 28084 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 96 178 3344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693252
X-RAY DIFFRACTIONf_angle_d0.97964455
X-RAY DIFFRACTIONf_chiral_restr0.0553529
X-RAY DIFFRACTIONf_plane_restr0.0071560
X-RAY DIFFRACTIONf_dihedral_angle_d14.39931155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30811260.30342073X-RAY DIFFRACTION92.86
1.95-2.020.33071310.29632196X-RAY DIFFRACTION94.98
2.02-2.090.33061210.25522229X-RAY DIFFRACTION96.51
2.09-2.170.32541080.2672173X-RAY DIFFRACTION97.02
2.17-2.270.25331340.24632223X-RAY DIFFRACTION97.04
2.27-2.390.28921320.22712192X-RAY DIFFRACTION97.52
2.39-2.540.3041250.22812242X-RAY DIFFRACTION97.81
2.54-2.740.2431860.22152294X-RAY DIFFRACTION98.18
2.74-3.010.23511910.20612194X-RAY DIFFRACTION98.31
3.01-3.450.23331880.19012167X-RAY DIFFRACTION98.37
3.45-4.340.14661280.16192241X-RAY DIFFRACTION98.71
4.34-31.880.19721700.17072220X-RAY DIFFRACTION99.05

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