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- PDB-2vn8: Crystal structure of human Reticulon 4 interacting protein 1 in c... -

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Basic information

Entry
Database: PDB / ID: 2vn8
TitleCrystal structure of human Reticulon 4 interacting protein 1 in complex with NADPH
ComponentsRETICULON-4-INTERACTING PROTEIN 1
KeywordsRECEPTOR INHIBITOR / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / ubiquinone biosynthetic process / regulation of dendrite development / nervous system development / mitochondrial outer membrane / mitochondrial matrix / mitochondrion / zinc ion binding
Similarity search - Function
Reticulon-4-interacting protein 1 / : / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...Reticulon-4-interacting protein 1 / : / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-NDP / Reticulon-4-interacting protein 1, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPike, A.C.W. / Guo, K. / Elkins, J. / Ugochukwu, E. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Pike, A.C.W. / Guo, K. / Elkins, J. / Ugochukwu, E. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Reticulon 4 Interacting Protein 1 in Complex with Nadph
Authors: Pike, A.C.W. / Guo, K. / Elkins, J. / Ugochukwu, E. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Oppermann, U.
History
DepositionJan 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETICULON-4-INTERACTING PROTEIN 1
B: RETICULON-4-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3457
Polymers82,5472
Non-polymers1,7985
Water5,098283
1
A: RETICULON-4-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2344
Polymers41,2731
Non-polymers9613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RETICULON-4-INTERACTING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1113
Polymers41,2731
Non-polymers8382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.950, 106.950, 177.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A-3 - 62
2114B-3 - 62
1216A63 - 69
2216B63 - 69
1314A70 - 103
2314B70 - 103
1414A114 - 256
2414B114 - 256
1516A257 - 265
2516B257 - 265
1614A266 - 331
2614B266 - 331
1716A332 - 336
2716B332 - 336
1814A337 - 396
2814B337 - 396

NCS oper: (Code: given
Matrix: (0.36214, -0.7941, -0.48811), (-0.82926, -0.5136, 0.22032), (-0.42565, 0.32499, -0.84451)
Vector: 115.2736, 10.98704, 324.82294)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RETICULON-4-INTERACTING PROTEIN 1 / NOGO-INTERACTING MITOCHONDRIAL PROTEIN


Mass: 41273.438 Da / Num. of mol.: 2 / Fragment: RESIDUES 45-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8WWV3

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.55 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 5.6
Details: 36% MPD, 0.135M AMMONIUM ACETATE, 0.09M SODIUM CITRATE PH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98074
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98074 Å / Relative weight: 1
ReflectionResolution: 2.1→64 Å / Num. obs: 68709 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 36.45 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.364 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1698 2.5 %RANDOM
Rwork0.175 ---
obs0.176 66949 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å21.21 Å20 Å2
2--2.42 Å20 Å2
3----3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 116 283 5799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225665
X-RAY DIFFRACTIONr_bond_other_d0.0010.023691
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9717729
X-RAY DIFFRACTIONr_angle_other_deg1.2573.0028982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60824.14215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7861522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021112
X-RAY DIFFRACTIONr_nbd_refined0.2030.2991
X-RAY DIFFRACTIONr_nbd_other0.2360.23529
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22737
X-RAY DIFFRACTIONr_nbtor_other0.1160.22587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.20533537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.40955698
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.09782128
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.232112031
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4044medium positional0.240.5
245loose positional0.855
4044medium thermal1.012
245loose thermal1.2710
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 122
Rwork0.261 4556
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)
11.65230.33760.53352.4834-1.47224.3354-0.0354-0.46260.12660.12950.02870.4042-0.0173-0.51820.0067-0.08820.06850.001-0.211-0.0467-0.142134.87413.4501145.1772
23.1553-1.2110.01012.12030.0662.2856-0.0972-0.24250.22010.05830.0526-0.0226-0.19530.38020.0446-0.0816-0.007-0.0472-0.31830.0072-0.235549.67683.9155137.1468
31.7224-0.54311.08070.7378-0.19052.1389-0.0114-0.0108-0.18850.00210.0229-0.0270.27090.3149-0.0116-0.00290.0718-0.0075-0.20810.0107-0.178756.792-8.3864139.7164
40.5685-0.0054-0.20742.7638-2.12578.15030.0675-0.15330.3337-0.1702-0.04610.5691-0.8116-1.443-0.02140.18580.306-0.12610.2155-0.19820.045653.568510.5182186.4284
53.4174-1.1129-1.32491.460.96024.8959-0.0585-0.2255-0.13770.0912-0.09110.1230.2038-0.25550.1496-0.01610.0597-0.0705-0.0806-0.074-0.179466.9325-4.5729190.7268
61.1142-0.93390.00241.64750.94414.41320.0373-0.1850.2404-0.06750.0225-0.2462-0.3980.2584-0.0598-0.00390.045-0.0555-0.1585-0.0604-0.102374.0005-1.0146179.5527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 100
2X-RAY DIFFRACTION2A101 - 242
3X-RAY DIFFRACTION3A243 - 396
4X-RAY DIFFRACTION4B-2 - 129
5X-RAY DIFFRACTION5B130 - 244
6X-RAY DIFFRACTION6B245 - 396

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