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- PDB-4ole: Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo ... -

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Basic information

Entry
Database: PDB / ID: 4ole
TitleCrystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution
ComponentsNext to BRCA1 gene 1 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ig-like domain from next to BRCA1 gene / PF16158 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


regulation of bone mineralization / phagophore assembly site / M band / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / negative regulation of osteoblast differentiation / autophagosome / Pexophagy / ubiquitin binding ...regulation of bone mineralization / phagophore assembly site / M band / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / negative regulation of osteoblast differentiation / autophagosome / Pexophagy / ubiquitin binding / macroautophagy / mitochondrial intermembrane space / late endosome / lysosome / receptor complex / nuclear body / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / membrane / cytosol
Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Next to BRCA1 gene 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _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: Next to BRCA1 gene 1 protein
B: Next to BRCA1 gene 1 protein
C: Next to BRCA1 gene 1 protein
D: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32020
Polymers55,0894
Non-polymers1,23116
Water10,449580
1
A: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2477
Polymers13,7721
Non-polymers4746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0264
Polymers13,7721
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9584
Polymers13,7721
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0885
Polymers13,7721
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Next to BRCA1 gene 1 protein
hetero molecules

D: Next to BRCA1 gene 1 protein
hetero molecules

D: Next to BRCA1 gene 1 protein
hetero molecules

D: Next to BRCA1 gene 1 protein
hetero molecules

A: Next to BRCA1 gene 1 protein
B: Next to BRCA1 gene 1 protein
C: Next to BRCA1 gene 1 protein
hetero molecules

A: Next to BRCA1 gene 1 protein
B: Next to BRCA1 gene 1 protein
C: Next to BRCA1 gene 1 protein
hetero molecules

A: Next to BRCA1 gene 1 protein
B: Next to BRCA1 gene 1 protein
C: Next to BRCA1 gene 1 protein
hetero molecules

A: Next to BRCA1 gene 1 protein
B: Next to BRCA1 gene 1 protein
C: Next to BRCA1 gene 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,28080
Polymers220,35616
Non-polymers4,92464
Water28816
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/21
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area34290 Å2
ΔGint-402 kcal/mol
Surface area88950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.457, 111.457, 230.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Next to BRCA1 gene 1 protein / Cell migration-inducing gene 19 protein / Membrane component chromosome 17 surface marker 2 / ...Cell migration-inducing gene 19 protein / Membrane component chromosome 17 surface marker 2 / Neighbor of BRCA1 gene 1 protein / Protein 1A1-3B


Mass: 13772.229 Da / Num. of mol.: 4 / Fragment: UNP residues 365-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 1A13B, BC009808, KIAA0049, M17S2, MIG19, NBR1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q14596
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (365-485) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (365-485) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 6.5 Å3/Da / Density % sol: 81.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.33
Details: 2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97891,0.97949,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978911
20.979491
30.918371
ReflectionResolution: 2.52→48.72 Å / Num. obs: 50067 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.76 % / Biso Wilson estimate: 61.165 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.52-2.619.011.2222.0944101489499.9
2.61-2.710.862.9418224723100
2.71-2.840.5953.9425785188100
2.84-2.990.4045.945565494299.9
2.99-3.170.2668.5435344778100
3.17-3.420.1513.8457075072100
3.42-3.760.09319.6411394950100
3.76-4.30.06427.8462795029100
4.3-5.40.05631.243207505699.8
5.4-48.720.0563444593543599.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.52→48.72 Å / Cor.coef. Fo:Fc: 0.9329 / Cor.coef. Fo:Fc free: 0.9389 / Occupancy max: 1 / Occupancy min: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 2532 5.07 %RANDOM
Rwork0.1729 ---
obs0.1737 49908 99.94 %-
Displacement parametersBiso max: 165.53 Å2 / Biso mean: 51.4814 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--3.0385 Å20 Å20 Å2
2---3.0385 Å20 Å2
3---6.077 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.52→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 71 580 4382
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1811SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes591HARMONIC5
X-RAY DIFFRACTIONt_it4113HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion523SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4699SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4113HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5595HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion2.34
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2494 191 5.27 %
Rwork0.2226 3431 -
all0.2241 3622 -
obs--99.94 %
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)
11.29120.0917-0.55992.2628-1.35922.1541-0.1096-0.2479-0.07620.1344-0.0488-0.33340.14020.28640.15850.029-0.0473-0.0054-0.04980.0106-0.089122.232111.245682.8426
21.09942.2871-1.92683.177-2.46582.19760.1660.05120.16370.26190.10980.3721-0.199-0.2224-0.2758-0.0387-0.00030.0605-0.02470.0649-0.002824.934443.499162.3249
30.0048-0.02570.860.4853-1.16785.4548-0.1729-0.33430.11850.27840.03160.003-0.5425-0.40860.14130.05650.0603-0.02930.0479-0.0563-0.17675.154622.4306101.295
43.2389-1.82650.59162.204-0.43310.9294-0.13020.25070.4677-0.0666-0.0287-0.1418-0.18790.03930.1589-0.0136-0.0103-0.0486-0.08870.0362-0.0269-4.687818.412560.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 485}A0 - 485
2X-RAY DIFFRACTION2{B|0 - 483}B0 - 483
3X-RAY DIFFRACTION3{C|0 - 482}C0 - 482
4X-RAY DIFFRACTION4{D|0 - 482}D0 - 482

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