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- PDB-1n0x: Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody i... -

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Basic information

Entry
Database: PDB / ID: 1n0x
TitleCrystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope
Components
  • (IMMUNOGLOBULIN ...) x 2
  • B2.1 peptide
KeywordsIMMUNE SYSTEM / antibody-peptide complex / peptide dimer
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / 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 / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma 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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Immunoglobulin gamma-1 heavy chain / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaphire, E.O. / Montero, M. / Menendez, A. / Irving, M.B. / Zwick, M.B. / Parren, P.W.H.I. / Burton, D.R. / Scott, J.K. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a Peptide Mimotope
Authors: Saphire, E.O. / Montero, M. / Menendez, A. / Irving, M.B. / Zwick, M.B. / Parren, P.W.H.I. / Burton, D.R. / Scott, J.K. / Wilson, I.A.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_name_com.name ..._entity.pdbx_fragment / _entity_name_com.name / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of ...Sequence The Genbank database sequence (AAA52919) is the correct match for the variable portion of the heavy chain except that the N-terminus has been changed from LEQSGAE to QVQLVQSGAE in the process of cloning from the recombinant Fab fragment to the IgG. The constant domains of the heavy chains H and K have the same sequence as all human IgG1 antibodies. The variable region of the light chain matches the Genbank database sequence (AAA52920) except that the N-terminus was changed in cloning to the IgG from ELTQAPG to EIVLTQSPG; the constant domains of the light chains L and M have the same sequence as all human kappa light chains. The authors maintain that the sequence of L and M, residue ALA 34 should be an ALA and not ARG (residue 33 in the sequence database).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN LIGHT CHAIN
H: IMMUNOGLOBULIN HEAVY CHAIN
M: IMMUNOGLOBULIN LIGHT CHAIN
K: IMMUNOGLOBULIN HEAVY CHAIN
P: B2.1 peptide
R: B2.1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,76820
Polymers102,3866
Non-polymers1,38114
Water13,061725
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.621, 184.358, 56.173
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211
DetailsFab #1 is comprised of chains L and H. Fab #2 is comprised of chains M and K. / The peptide chains P and R form a dimer. Peptide chain P binds Fab #1 (LH) Peptide chain R binds Fab #2 (MK)

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Components

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Protein/peptide , 1 types, 2 molecules PR

#3: Protein/peptide B2.1 peptide


Mass: 2546.900 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: selected from phage display peptide library, then chemically synthesized.
Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 4 molecules LMHK

#1: Antibody IMMUNOGLOBULIN LIGHT CHAIN / IGG


Mass: 23707.354 Da / Num. of mol.: 2 / Fragment: UNP residues 132-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO K1 / References: UniProt: Q8TCD0, UniProt: P01834*PLUS
#2: Antibody IMMUNOGLOBULIN HEAVY CHAIN / IGG / Immunoglobulin gamma-1 heavy chain NIE


Mass: 24938.898 Da / Num. of mol.: 2 / Fragment: UNP residues 117-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO K1 / References: UniProt: P0DOX5

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Non-polymers , 5 types, 739 molecules

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


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 725 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: ammonium sulfate, lithium sulfate, CAPS buffer, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 171 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2000 / Details: flat mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.78→33.45 Å / Num. all: 94383 / Num. obs: 84895 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.6
Reflection shellResolution: 1.78→1.81 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 4468 / Rsym value: 0.385 / % possible all: 87.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab domains from uncomplexed IgG1 b12 structure (1HZH)

1hzh


Resolution: 1.8→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 10% test set (9419) reflections selected for initial rounds of refinement. For final round of refinement, a 2% test set was randomly selected from reflections contained in the original 10% test set.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1967 -random
Rwork0.22 ---
all0.229 94383 --
obs0.229 84895 92 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.34 Å2
2--2.678 Å20 Å2
3----3.268 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 83 725 7899

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