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- PDB-3u7w: Crystal structure of NIH45-46 Fab -

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Basic information

Entry
Database: PDB / ID: 3u7w
TitleCrystal structure of NIH45-46 Fab
Components
  • Heavy chain, Ig gamma-1 chain C region
  • Light chain, Ig kappa chain C region
KeywordsIMMUNE SYSTEM / Ig fold / Antibody / HIV gp120
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / 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 ...: / : / 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 kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDiskin, R. / Bjorkman, P.J.
CitationJournal: Science / Year: 2011
Title: Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design.
Authors: Diskin, R. / Scheid, J.F. / Marcovecchio, P.M. / West, A.P. / Klein, F. / Gao, H. / Gnanapragasam, P.N. / Abadir, A. / Seaman, M.S. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Refinement description
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / software / struct_conn / struct_ref_seq
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_end
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain, Ig gamma-1 chain C region
L: Light chain, Ig kappa chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6837
Polymers48,0902
Non-polymers5945
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-38 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.380, 87.390, 166.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain, Ig gamma-1 chain C region


Mass: 25089.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK 2936E / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Antibody Light chain, Ig kappa chain C region


Mass: 23000.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Cell line (production host): HEK 2936E / Production host: Homo sapiens (human) / References: UniProt: P01834

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 129 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% polyethylene glycol 20,000, 0.1 M sodium acetate pH 5.0, 0.1 M sodium/potassium tartrate, 0.02 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→38.8 Å / Num. all: 22923 / Num. obs: 22795 / % possible obs: 99.5 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.6929199.3
2.6929-2.8007199
2.8007-2.9281199.8
2.9281-3.0824199.5
3.0824-3.2755199.4
3.2755-3.5282198.1
3.5282-3.883199.5
3.883-4.4441198.3
4.4441-5.5964199.2
5.5964-38.6889198

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_805)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NGB

3ngb


Resolution: 2.6→38.685 Å / SU ML: 0.89 / σ(F): 1.34 / Phase error: 23.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1136 5.01 %5%
Rwork0.1841 ---
all0.187 22923 --
obs0.1868 22692 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.819 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3458 Å2-0 Å20 Å2
2---1.8509 Å2-0 Å2
3---2.1967 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 37 125 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043503
X-RAY DIFFRACTIONf_angle_d0.8384747
X-RAY DIFFRACTIONf_dihedral_angle_d14.0291270
X-RAY DIFFRACTIONf_chiral_restr0.057516
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.39261390.34532640X-RAY DIFFRACTION99
2.7183-2.86160.33941400.2732647X-RAY DIFFRACTION100
2.8616-3.04080.26951410.21372672X-RAY DIFFRACTION100
3.0408-3.27550.22651410.18342684X-RAY DIFFRACTION100
3.2755-3.60490.26161400.18222648X-RAY DIFFRACTION98
3.6049-4.1260.23011410.17222722X-RAY DIFFRACTION99
4.126-5.19630.17621450.132693X-RAY DIFFRACTION99
5.1963-38.68890.22371490.18222850X-RAY DIFFRACTION98
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)
10.3732-0.48080.90454.6362-1.2692.0924-0.1384-0.0133-0.1997-0.04620.38010.79990.1821-0.4039-0.20950.1721-0.02970.05310.34630.03590.32899.3457.49511.7049
25.5691-0.95821.80332.00251.44942.2728-0.2675-0.1743-0.08020.16610.3218-0.01760.1217-0.4585-0.02370.12790.02190.01990.2581-0.05150.181218.801314.3983.9234
31.75451.659-0.4632.27920.39072.4353-0.08080.1733-0.1806-0.1182-0.0175-0.13330.10530.1570.08120.17460.07210.0250.2948-0.00670.219420.768811.3858-0.3401
42.19981.8653-1.88951.8712-2.04813.7725-0.17030.23840.02670.03410.3110.33530.2347-0.4642-0.15690.26050.02250.03980.31130.04640.31315.22473.299514.2888
53.17020.14890.09824.3084-1.10110.5362-0.2022-0.7755-0.08391.12350.24210.62010.2567-0.2012-0.2280.61090.04390.24830.37240.13520.4556-6.8976-3.136437.7543
61.45081.0624-0.10131.42630.57632.70140.0534-0.14930.32810.26640.35540.757-0.3411-0.7741-0.24490.47430.1210.20970.40060.20140.4876-7.00021.599928.6152
76.32651.2081-0.4153.6958-0.13697.5045-0.0740.1798-0.03340.59910.12750.7720.3985-1.30260.05430.53290.02880.17390.76330.19480.8616-15.8058-6.234331.4761
85.8684-1.3767-2.07184.42210.17472.9241-0.6057-0.6143-0.68120.8934-0.0870.24460.48650.21130.63280.25780.03210.01010.39390.09010.253623.203616.852226.7698
93.0499-1.2083-4.12122.85970.39976.3821-0.3032-0.2650.20750.54980.187-0.23860.12360.41670.15040.31440.0229-0.00020.19110.0180.217727.740619.354719.2101
102.98140.4638-0.86448.82390.17585.85340.1542-0.20770.3746-0.06220.1830.7569-0.1343-0.6609-0.22450.29910.03670.02660.42350.08850.273418.285326.39216.6686
116.5619-6.0421-4.62037.54474.82713.83670.4055-0.59050.20840.2799-0.0136-0.6032-0.55921.197-0.26850.4029-0.1233-0.00550.49550.05460.298229.48625.153923.3987
121.04840.6471-0.70320.6834-0.35650.41940.00270.02030.19820.4717-0.11480.20710.0952-0.3558-0.09740.29150.07180.07310.33010.010.257217.066717.400426.3603
130.89760.6064-0.3425.3717-0.14791.6092-0.1584-0.11180.0091-0.1690.2495-0.1231-0.0880.02-0.08260.38340.03360.18510.30310.03340.36223.2952-2.332938.0225
142.69952.5733-0.81523.0784-0.81151.7910.0349-0.146-0.44220.1353-0.083-0.52930.27170.01950.15120.41220.0460.16930.24820.07870.32112.8776-10.437742.9505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 2:25)
2X-RAY DIFFRACTION2chain 'H' and (resseq 26:45)
3X-RAY DIFFRACTION3chain 'H' and (resseq 46:103)
4X-RAY DIFFRACTION4chain 'H' and (resseq 104:128)
5X-RAY DIFFRACTION5chain 'H' and (resseq 129:149)
6X-RAY DIFFRACTION6chain 'H' and (resseq 150:207)
7X-RAY DIFFRACTION7chain 'H' and (resseq 208:221)
8X-RAY DIFFRACTION8chain 'L' and (resseq 1:18)
9X-RAY DIFFRACTION9chain 'L' and (resseq 19:36)
10X-RAY DIFFRACTION10chain 'L' and (resseq 37:59)
11X-RAY DIFFRACTION11chain 'L' and (resseq 60:73)
12X-RAY DIFFRACTION12chain 'L' and (resseq 74:113)
13X-RAY DIFFRACTION13chain 'L' and (resseq 114:174)
14X-RAY DIFFRACTION14chain 'L' and (resseq 175:214)

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