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- PDB-2h32: Crystal structure of the pre-B cell receptor -

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Basic information

Entry
Database: PDB / ID: 2h32
TitleCrystal structure of the pre-B cell receptor
Components
  • Immunoglobulin heavy chain
  • Immunoglobulin iota chain
  • Immunoglobulin omega chain
KeywordsIMMUNE SYSTEM / beta sheets / v and c-type Ig folds
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Cell surface interactions at the vascular wall / immune response / endoplasmic reticulum / extracellular space / extracellular region / membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin iota chain / Immunoglobulin lambda-like polypeptide 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBankovich, A.J.
CitationJournal: Science / Year: 2007
Title: Structural Insight into Pre-B Cell Receptor Function
Authors: Bankovich, A.J. / Raunser, S. / Juo, Z.S. / Walz, T. / Davis, M.M. / Garcia, K.C.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Chain H is an antibody heavy chain which includes hypervariable regions, therefore it does ...SEQUENCE Chain H is an antibody heavy chain which includes hypervariable regions, therefore it does not match any of the sequences in the UNP sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin iota chain
B: Immunoglobulin omega chain
H: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3085
Polymers52,1773
Non-polymers1312
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-76 kcal/mol
Surface area21440 Å2
MethodPISA
2
A: Immunoglobulin iota chain
B: Immunoglobulin omega chain
H: Immunoglobulin heavy chain
hetero molecules

A: Immunoglobulin iota chain
B: Immunoglobulin omega chain
H: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,61610
Polymers104,3556
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area14360 Å2
ΔGint-188 kcal/mol
Surface area40430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.502, 71.502, 217.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Immunoglobulin iota chain / Vpre / B protein / VpreB protein / CD179a antigen


Mass: 14553.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPREB1, VPREB / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P12018
#2: Protein Immunoglobulin omega chain / Immunoglobulin- related protein 14.1 / Immunoglobulin lambda-like polypeptide 1 / Ig lambda-5 / CD179b antigen


Mass: 13128.717 Da / Num. of mol.: 1 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLL1, IGL1 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15814
#3: Antibody Immunoglobulin heavy chain /


Mass: 24495.428 Da / Num. of mol.: 1 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / pH: 7
Details: 12% MP5K, 200mM Zinc acetate, 100mM PIPES, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. obs: 16403 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rsym value: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.368 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
PHASERphasing
CNSrefinement
HKL-2000data scaling
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1IT9 AND 1ADQ

1it9

1adq


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.888 / SU B: 25.731 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.111 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 824 5.1 %RANDOM
Rwork0.267 ---
obs0.269 15425 99.7 %-
all-14658 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--2.73 Å20 Å2
3----5.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 2 106 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9554712
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.465434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03123.813139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61715540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6881517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.21666
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22276
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2163
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2420.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.250.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.52244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36423542
X-RAY DIFFRACTIONr_scbond_it1.91831416
X-RAY DIFFRACTIONr_scangle_it2.7844.51170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 68 -
Rwork0.367 1092 -
obs--100 %
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)
10.4014-0.09110.34010.73340.23832.2491-0.09650.1027-0.00170.04030.0114-0.0122-0.0616-0.07610.0852-0.064-0.0189-0.00580.0947-0.0171-0.06067.296-13.386635.3686
22.0415-0.34360.40873.50242.06724.51230.01530.13060.4123-0.1608-0.0067-0.0103-0.50110.1623-0.00860.17650.0109-0.090.12020.1031-0.11452.217611.090110.9554
33.1863-2.24612.15464.2298-3.61937.41470.08750.0958-0.1347-0.3307-0.08660.1389-0.4036-0.793-0.0010.22830.1862-0.13110.1595-0.1626-0.1335-14.207712.922416.0855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1111 - 111
2X-RAY DIFFRACTION1BB56 - 711 - 16
3X-RAY DIFFRACTION1HC1 - 1191 - 119
4X-RAY DIFFRACTION2BB72 - 17217 - 117
5X-RAY DIFFRACTION3HC120 - 223120 - 223

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