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- PDB-6wp0: The Crystal Structure of Domain-Swapped Trimer Q108K:T51D variant... -

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Basic information

Entry
Database: PDB / ID: 6wp0
TitleThe Crystal Structure of Domain-Swapped Trimer Q108K:T51D variant of HCRBPII
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / iLBP
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
ACETATE ION / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
Citation
Journal: Chembiochem / Year: 2020
Title: Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.
Authors: Ghanbarpour, A. / Santos, E.M. / Pinger, C. / Assar, Z. / Hossaini Nasr, S. / Vasileiou, C. / Spence, D. / Borhan, B. / Geiger, J.H.
#1: Journal: To Be Published
Title: The Crystal Structure of Apo Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F variant of HCRBPII
Authors: Ghanbarpour, A. / Geiger, J.
History
DepositionApr 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
C: Retinol-binding protein 2
D: Retinol-binding protein 2
E: Retinol-binding protein 2
F: Retinol-binding protein 2
G: Retinol-binding protein 2
H: Retinol-binding protein 2
I: Retinol-binding protein 2
J: Retinol-binding protein 2
K: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,40235
Polymers187,35012
Non-polymers2,05223
Water1,13563
1
A: Retinol-binding protein 2
I: Retinol-binding protein 2
K: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3909
Polymers46,8373
Non-polymers5536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-61 kcal/mol
Surface area20420 Å2
MethodPISA
2
B: Retinol-binding protein 2
J: Retinol-binding protein 2
L: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,81714
Polymers46,8373
Non-polymers98011
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-63 kcal/mol
Surface area21140 Å2
MethodPISA
3
C: Retinol-binding protein 2
E: Retinol-binding protein 2
G: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1146
Polymers46,8373
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-62 kcal/mol
Surface area20910 Å2
MethodPISA
4
D: Retinol-binding protein 2
F: Retinol-binding protein 2
H: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0816
Polymers46,8373
Non-polymers2433
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-60 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.565, 111.272, 101.826
Angle α, β, γ (deg.)90.000, 112.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRILEILE(chain 'A' and (resid 1 or (resid 2 and (name...AA1 - 251 - 25
12PHEPHESERSER(chain 'A' and (resid 1 or (resid 2 and (name...AA27 - 5527 - 55
13PHEPHELYSLYS(chain 'A' and (resid 1 or (resid 2 and (name...AA57 - 13257 - 132
24THRTHRILEILE(chain 'B' and (resid 1 or (resid 2 and (name...BB1 - 251 - 25
25PHEPHESERSER(chain 'B' and (resid 1 or (resid 2 and (name...BB27 - 5527 - 55
26PHEPHELYSLYS(chain 'B' and (resid 1 or (resid 2 and (name...BB57 - 13257 - 132
37THRTHRILEILE(chain 'C' and (resid 1 or (resid 2 and (name...CC1 - 251 - 25
38PHEPHESERSER(chain 'C' and (resid 1 or (resid 2 and (name...CC27 - 5527 - 55
39PHEPHELYSLYS(chain 'C' and (resid 1 or (resid 2 and (name...CC57 - 13257 - 132
410THRTHRILEILE(chain 'D' and (resid 1 or (resid 2 and (name...DD1 - 251 - 25
411PHEPHESERSER(chain 'D' and (resid 1 or (resid 2 and (name...DD27 - 5527 - 55
412PHEPHELYSLYS(chain 'D' and (resid 1 or (resid 2 and (name...DD57 - 13257 - 132
513THRTHRILEILE(chain 'E' and (resid 1 or (resid 2 and (name...EE1 - 251 - 25
514PHEPHESERSER(chain 'E' and (resid 1 or (resid 2 and (name...EE27 - 5527 - 55
515PHEPHELYSLYS(chain 'E' and (resid 1 or (resid 2 and (name...EE57 - 13257 - 132
616THRTHRILEILE(chain 'F' and (resid 1 or (resid 2 and (name...FF1 - 251 - 25
617PHEPHESERSER(chain 'F' and (resid 1 or (resid 2 and (name...FF27 - 5527 - 55
618PHEPHELYSLYS(chain 'F' and (resid 1 or (resid 2 and (name...FF57 - 13257 - 132
719THRTHRILEILE(chain 'G' and (resid 1 through 8 or (resid 9...GG1 - 251 - 25
720PHEPHESERSER(chain 'G' and (resid 1 through 8 or (resid 9...GG27 - 5527 - 55
721PHEPHELYSLYS(chain 'G' and (resid 1 through 8 or (resid 9...GG57 - 13257 - 132
822THRTHRILEILE(chain 'H' and (resid 1 or (resid 2 and (name...HH1 - 251 - 25
823PHEPHESERSER(chain 'H' and (resid 1 or (resid 2 and (name...HH27 - 5527 - 55
824PHEPHELYSLYS(chain 'H' and (resid 1 or (resid 2 and (name...HH57 - 13257 - 132
925THRTHRILEILE(chain 'I' and (resid 1 or (resid 2 and (name...II1 - 251 - 25
926PHEPHESERSER(chain 'I' and (resid 1 or (resid 2 and (name...II27 - 5527 - 55
927PHEPHELYSLYS(chain 'I' and (resid 1 or (resid 2 and (name...II57 - 13257 - 132
1028THRTHRILEILE(chain 'J' and (resid 1 or (resid 2 and (name...JJ1 - 251 - 25
1029PHEPHESERSER(chain 'J' and (resid 1 or (resid 2 and (name...JJ27 - 5527 - 55
1030PHEPHELYSLYS(chain 'J' and (resid 1 or (resid 2 and (name...JJ57 - 13257 - 132
1131THRTHRILEILE(chain 'K' and (resid 1 through 8 or (resid 9...KK1 - 251 - 25
1132PHEPHESERSER(chain 'K' and (resid 1 through 8 or (resid 9...KK27 - 5527 - 55
1133PHEPHELYSLYS(chain 'K' and (resid 1 through 8 or (resid 9...KK57 - 13257 - 132
1234THRTHRILEILE(chain 'L' and (resid 1 through 4 or (resid 5...LL1 - 251 - 25
1235PHEPHESERSER(chain 'L' and (resid 1 through 4 or (resid 5...LL27 - 5527 - 55
1236PHEPHELYSLYS(chain 'L' and (resid 1 through 4 or (resid 5...LL57 - 13257 - 132

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Components

#1: Protein
Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15612.487 Da / Num. of mol.: 12 / Mutation: Q108K, T51D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, ammonium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.78→46.9 Å / Num. obs: 43694 / % possible obs: 99.34 % / Redundancy: 7.5 % / Biso Wilson estimate: 60.64 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.5
Reflection shellResolution: 2.78→2.879 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4222 / % possible all: 96.99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rct

2rct


Resolution: 2.78→46.9 Å / SU ML: 0.5618 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.98 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3205 1986 4.56 %
Rwork0.2757 41563 -
obs0.2777 43549 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.42 Å2
Refinement stepCycle: LAST / Resolution: 2.78→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12702 0 134 68 12904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002813042
X-RAY DIFFRACTIONf_angle_d0.700517579
X-RAY DIFFRACTIONf_chiral_restr0.04571915
X-RAY DIFFRACTIONf_plane_restr0.00322264
X-RAY DIFFRACTIONf_dihedral_angle_d16.74187663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.4411400.36622868X-RAY DIFFRACTION95.95
2.85-2.930.4411390.35592954X-RAY DIFFRACTION99.65
2.93-3.010.44641470.35422958X-RAY DIFFRACTION99.71
3.01-3.110.4321480.35382962X-RAY DIFFRACTION99.84
3.11-3.220.38951410.33162950X-RAY DIFFRACTION99.55
3.22-3.350.41481420.3192973X-RAY DIFFRACTION99.81
3.35-3.50.35571370.29332975X-RAY DIFFRACTION99.78
3.5-3.690.30831410.28192983X-RAY DIFFRACTION99.62
3.69-3.920.30741410.2742947X-RAY DIFFRACTION99.68
3.92-4.220.27881500.24623001X-RAY DIFFRACTION99.81
4.22-4.640.26631400.22212967X-RAY DIFFRACTION99.81
4.64-5.320.25981390.23413007X-RAY DIFFRACTION99.75
5.32-6.70.30241410.26922982X-RAY DIFFRACTION99.65
6.7-49.60.30271400.2663036X-RAY DIFFRACTION98.57
Refinement TLS params.Method: refined / Origin x: 13.4355609933 Å / Origin y: 6.86166188511 Å / Origin z: 23.5147586679 Å
111213212223313233
T0.518003653238 Å20.00660613163523 Å2-0.0304322084404 Å2-0.517392493324 Å20.00984290288408 Å2--0.638629237229 Å2
L0.153244001715 °2-0.0360522046755 °2-0.0219309507782 °2-0.0418070296342 °20.0262290906016 °2--0.0813589211991 °2
S-0.0108282719839 Å °0.00119408936274 Å °-0.0604988774534 Å °0.0398509797555 Å °-0.0210331384652 Å °-0.00267713967202 Å °0.0242531264799 Å °-0.00260275565397 Å °0.0249813998224 Å °
Refinement TLS groupSelection details: all

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