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- PDB-4x8y: Crystal structure of human PGRMC1 cytochrome b5-like domain -

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Basic information

Entry
Database: PDB / ID: 4x8y
TitleCrystal structure of human PGRMC1 cytochrome b5-like domain
ComponentsMembrane-associated progesterone receptor component 1
KeywordsMEMBRANE PROTEIN / Receptor / Membrane
Function / homology
Function and homology information


smooth endoplasmic reticulum membrane / neutrophil degranulation / heme biosynthetic process / plasma membrane => GO:0005886 / endomembrane system / specific granule membrane / steroid binding / amyloid-beta binding / cell body / mitochondrial outer membrane ...smooth endoplasmic reticulum membrane / neutrophil degranulation / heme biosynthetic process / plasma membrane => GO:0005886 / endomembrane system / specific granule membrane / steroid binding / amyloid-beta binding / cell body / mitochondrial outer membrane / neuron projection / neuronal cell body / synapse / heme binding / Neutrophil degranulation / endoplasmic reticulum / protein homodimerization activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Membrane-associated progesterone receptor component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsNakane, T. / Yamamoto, T. / Shimamura, T. / Kobayashi, T. / Kabe, Y. / Suematsu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology AgencyExploratory Research for Advanced Technology (ERATO) Suematsu Gas Biology Project Japan
CitationJournal: Nat Commun / Year: 2016
Title: Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
Authors: Kabe, Y. / Nakane, T. / Koike, I. / Yamamoto, T. / Sugiura, Y. / Harada, E. / Sugase, K. / Shimamura, T. / Ohmura, M. / Muraoka, K. / Yamamoto, A. / Uchida, T. / Iwata, S. / Yamaguchi, Y. / ...Authors: Kabe, Y. / Nakane, T. / Koike, I. / Yamamoto, T. / Sugiura, Y. / Harada, E. / Sugase, K. / Shimamura, T. / Ohmura, M. / Muraoka, K. / Yamamoto, A. / Uchida, T. / Iwata, S. / Yamaguchi, Y. / Krayukhina, E. / Noda, M. / Handa, H. / Ishimori, K. / Uchiyama, S. / Kobayashi, T. / Suematsu, M.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-associated progesterone receptor component 1
B: Membrane-associated progesterone receptor component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0164
Polymers29,7832
Non-polymers1,2332
Water1,964109
1
A: Membrane-associated progesterone receptor component 1
hetero molecules

A: Membrane-associated progesterone receptor component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0164
Polymers29,7832
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x+1/2,y,-z+7/41
Buried area2350 Å2
ΔGint-38 kcal/mol
Surface area12550 Å2
MethodPISA
2
B: Membrane-associated progesterone receptor component 1
hetero molecules

B: Membrane-associated progesterone receptor component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0164
Polymers29,7832
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_556-y+1/2,-x+1/2,-z+3/21
Buried area2620 Å2
ΔGint-38 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.230, 167.230, 63.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Membrane-associated progesterone receptor component 1 / mPR


Mass: 14891.333 Da / Num. of mol.: 2 / Fragment: UNP residues 72-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGRMC1, HPR6.6, PGRMC / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00264
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.26M ammonium sulfate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 30, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 33013 / Num. obs: 32298 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 11.19 % / Biso Wilson estimate: 40.631 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.83
Reflection shellResolution: 1.95→2 Å / Redundancy: 11.21 % / Rmerge(I) obs: 1.114 / Mean I/σ(I) obs: 2.39 / Num. unique all: 2384 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXAutoSolmodel building
PHENIX(phenix.refine: dev_1426)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXAutoSolphasing
BSSdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.716 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 2153 6.67 %RANDOM
Rwork0.1834 ---
obs0.1853 32283 97.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.61 Å2 / Biso mean: 53.6645 Å2 / Biso min: 21.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 86 109 1963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081923
X-RAY DIFFRACTIONf_angle_d1.1642621
X-RAY DIFFRACTIONf_dihedral_angle_d16.193693
X-RAY DIFFRACTIONf_chiral_restr0.046251
X-RAY DIFFRACTIONf_plane_restr0.005340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99530.26381430.26062006214999
1.9953-2.04520.26531420.22252005214799
2.0452-2.10040.22591430.199219922135100
2.1004-2.16210.2461440.1941999214399
2.1621-2.23180.23531410.19022011215299
2.2318-2.31150.25651440.19061993213799
2.3115-2.40390.20921430.18842010215399
2.4039-2.51310.2231430.1781997214098
2.5131-2.64530.19841430.18381998214198
2.6453-2.81060.23911440.20222016216099
2.8106-3.02690.23951420.20091996213897
3.0269-3.33020.26321460.19492013215998
3.3302-3.8090.20061440.17612021216597
3.809-4.78760.17861430.15492009215296
4.7876-19.71690.18191480.17962064221294
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8369-0.46250.73133.2172-1.2486.40720.0249-0.08540.07430.13680.0286-0.0222-0.13190.0474-0.1370.2187-0.03560.03630.2552-0.01290.188350.7297-21.282971.1688
23.7682-4.73660.46936.5135-1.91973.4249-0.3136-0.5116-0.96970.64530.18910.66430.63360.01130.07640.53460.01460.02860.44590.09350.471947.3106-29.47661.4954
32.9335-0.22340.83844.61860.53546.28850.03690.2235-0.0935-0.1377-0.1665-0.40490.22350.83750.11410.2002-0.02750.0860.34960.03070.256458.4995-21.538862.0698
42.34461.958-0.41642.1125-1.19775.08730.26920.2621.46380.2860.07460.857-0.5806-0.2999-0.46110.6305-0.05460.12880.52440.03860.917152.5385-1.393158.5674
57.98310.01-2.68166.4179-2.42352.61330.3289-0.4281.17640.7282-0.06430.1603-0.42370.5264-0.25110.5276-0.23510.09560.4573-0.03770.584666.0205-0.593259.8754
62.60462.3456-1.45285.10911.6583.85950.36860.60481.6433-0.41010.12330.5691-0.7183-0.6642-0.4290.5961-0.20640.17230.48920.15790.961867.4027.15650.9242
73.2963-3.82341.46854.462-1.91581.90961.3747-0.46441.93990.8159-0.6401-1.1184-0.053-1.5766-0.77721.0607-0.10530.1040.80560.0631.080163.084314.140152.5884
82.7338-1.86170.5453.99134.28518.11110.2742-0.00450.755-0.735-0.24060.6938-0.308-1.18940.00291.2163-0.00190.08621.56190.55251.230459.59528.990743.1077
95.4443-4.98410.93275.8114-1.29770.3005-0.19690.9926-0.0596-0.51240.14770.32630.0745-0.09730.26880.5412-0.19730.0140.59660.08480.545862.819-3.5847.5583
100.0171-0.0584-0.12640.30510.63231.3131-0.13130.35310.20750.32610.30780.14380.25120.41260.0550.3444-0.16640.10060.55250.02560.674376.9777-0.249351.0709
115.06-3.07047.04549.152-4.66379.9562-0.03060.14480.28190.155-0.1177-0.0451-0.5867-0.0730.09410.30360.04380.0440.32880.00740.301543.8528-12.390560.1043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 68:126)A68 - 126
2X-RAY DIFFRACTION2chain 'A' and (resseq 127:141)A127 - 141
3X-RAY DIFFRACTION3chain 'A' and (resseq 142:179)A142 - 179
4X-RAY DIFFRACTION4chain 'B' and (resseq 65:80)B65 - 80
5X-RAY DIFFRACTION5chain 'B' and (resseq 81:113)B81 - 113
6X-RAY DIFFRACTION6chain 'B' and (resseq 114:132)B114 - 132
7X-RAY DIFFRACTION7chain 'B' and (resseq 133:137)B133 - 137
8X-RAY DIFFRACTION8chain 'B' and (resseq 138:146)B138 - 146
9X-RAY DIFFRACTION9chain 'B' and (resseq 147:173)B147 - 173
10X-RAY DIFFRACTION10chain 'B' and (resseq 500:500)B500
11X-RAY DIFFRACTION11chain 'A' and (resseq 500:500)A500

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